Supplementary Table 1. NAR Molecular Biology Database Collection: 2008 update

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Dec 4, 2013 (3 years and 6 months ago)

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Supplementary Table 1.

NAR Molecular Biology Database Collection
:

2008 update
a

No
b

Database name
c


Full name and/or description

URL


1. Nucleotide Sequence Databases




1.1. International Nucleotide Sequence Database Collaboration



1

DDBJ
-

DNA Data

Bank
of Japan

All known nucleotide and protein sequences

http://www.ddbj.nig.ac.jp

2

EMBL Nucleotide
Sequence Database

All known nucleotide and protein sequences

htt
p://www.ebi.ac.uk/embl.html

3

GenBank
®

All known nucleotide and protein sequences

http://www.ncbi.nlm.nih.gov/
Entrez


1.2.
Coding and coding DNA:
genes, motifs and regulatory sites



403

ACLAME

A

cla
ssificat
ion of genetic
m
obile
e
lements

http://aclame.ulb.ac.be/

337

CORG

C
o
mparative
R
egulatory
G
enomics:

conserved non
-
coding blocks

in vertebrate species

http://corg.molgen.mpg.
de

30

CUTG

C
odon
U
sage
T
abulated from
G
enBank

http://www.kazusa.or.jp/codon/

1157

ECRbase

Database of
E
volutionary
C
onserved
R
egions,
p
romoters, and
transcription factor binding si
tes

http://ecrbase.dcode.org/

668

Entrez Gene

Gene
-
centered information at NCBI

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gen
e

669

FESD

F
unctional
E
lement
S
NPs
D
atabase: SNPs located within
promoters, UTRs, etc., of human genes

http://sysbio.kribb.re.kr/FESD/



468

FREP

F
unctional
R
ep
eats in mouse cDNAs

http://facts.gsc.riken.go.jp/FREP/

480

Genetic Codes

Genetic codes in various organisms and organelles

http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.c
gi?mode=c

1079

GISSD

G
roup I
I
ntron
S
equence and
S
tructure

D
atabase

http://www.rna.whu.edu.cn/gissd

1083

GyDB

Gy
psy database of mobile genetic elements

http://gydb.uv.es/gydb/intro.htm

825

HumHot

Hum
an meiotic recom
bination
hot

spots

http://www.jncasr.ac.in/humhot/

932

InSatDb

Sequences and properties of
in
sect micro
sat
ellites

http://www.cdfd.org.in/insatdb

832

ISfinder

Insertion sequences from bacteria and archaea

http://www
-
is.biotoul.fr

512

Islander

Pathogenicity islands and prophages in bacterial genomes

http://www.indiana.edu/~islander

697

L1Base

Functional annotation and
prediction of LINE
-
1 elements

http://line1.molgen.mpg.de

19

MethDB

DNA methylation data, patterns and profiles

http://www.methdb.de

343

MICdb

Prokaryotic microsatellites

http://210.212.212.7/MIC/index.html

707

NPRD

Nucleosome
P
ositioning
R
egion
D
atabase

http://srs6
.bionet.nsc.ru/srs6bin/cgi
-
bin/wgetz?page+
LibInfo+
-
id+2Xnp11RCiPU+
-
lib+NUCLEOSOME

931

OriDB

DNA Replication
Ori
gin Database: Confirmed and predicted sites

http://www.oridb.org/

551

PACRAT

Archaeal and bacterial int
ergenic sequence features

No longer maintained

608

PANDIT

Protein and associated nucleotide domains with inferred trees

http://www.ebi.ac.uk/goldman
-
srv/pandit/

933

Patome

Annotated sequences from
patents and patent applications

http://www.patome.org

958

PolymiRTS

Polymorphism in microRNA Target Site

http://compbio.utmem.edu/miRSNP/

1007

PseudoGene.org

Pseudog
enes in eukaryotic and prokaryotic genomes

http://www.pseudogene.org/

21

RECODE

Genes using programmed translational recoding in their
expression

http://recode.gene
tics.utah.edu

391

RefSeq

Reference Sequence database: an
integrated, non
-
redundant set
of genomic DNA, RNA, and protein sequences

http://www.ncbi.nlm.nih.gov/RefSeq/

1019

RetrOryza

LTR
-
retrotransposons

in rice

http://www.retroryza.org

309

S/MARt DB

Nuclear scaffold/matrix attached regions

http://smartdb.bioinf.med.uni
-
goettingen.de/

1013

SNPSTR

Micro
satellite compound markers in 5 vertebrate genomes

http://www3.imperial.ac.uk/theoreticalgenomics/data
-
software

47

STRBase

Short tandem DNA repeats database

http://www.cstl.nist.gov/div831/strbase/

929

Synthetic Gene
DB

Synthetic genes described in peer
-
reviewed literature

http://www.evolvingcode.net/codon/sgdb
/index.php

588

TIGR plant repeat
DB

Classification of repetitive sequences in plant genomes

http://www.tigr.org/tdb/e2k1/plant.repeats

1141

TranspoGene

Transposed elements influence on the tran
scriptome of seven
vertebrates and invertebrates

http://transpogene.tau.ac.il/

1035

TRDB

Tandem repeats in genomic DNA

http://tandem.bu.edu/cgi
-
bin/trd
b/trdb.exe

1143

UgMicroSatdb

UniGene MicroSatellite database: short tandem repeats from
various eukaryotic genomes

http://ipu.ac.in/usbt/UgMicroSatdb.htm

320

UniVec

Vector sequences, adapters, linke
rs and primers used in DNA
cloning, used to check for vector contamination

http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html

252

UTRdb/UTRsite

5'
-

and 3'
-
UTRs of eukaryotic mRNAs

http://bighost.area.ba.cnr.it/BIG/UTRHome/

1146

UTRome

3'UTRs and their functional elements in C. elegans

http://www.utrome.org

302

Vectordb

Characterization and cla
ssification of nucleic acid vectors

http://seq.yeastgenome.org/vectordb/

968

VISTA Enhancer
Browser

Enhancer elements in the human genome

http://enhancer.lbl.gov/


1.3. Gene structure, introns and exons, splice sites



414

ASAP II

Comparative analysis of alternative splicing in animal species

http://bioinfo.mbi.ucla.edu/ASAP2/

10

ASDB

Alternative Splicing Datab
ase: protein products and expression
patterns of alternatively
-
spliced genes

http://hazelton.lbl.gov/~teplitski/alt/

639

ASHESdb

Alternatively Spliced Human genes by Exon Skipping

http://sege.ntu.edu.sg/wester/ashes/

28

ASTD

Alternative Splicing and Transcript Diversity database

http://www.ebi.ac.uk/astd/

920

ATD

Alternate transcript diversity database

S
uperseded by ASTD, no. 28

803

ChimerDB

Chimeric (fusion) sequences in human, rat and mouse

http://genome.ewha.ac.kr/ChimerDB/

450

EASED

Extended Alternatively Spliced EST Database

http://eased.bioinf.mdc
-
berlin.de/

667

ECgene

Genome annotation for alternative splicing

http://genome.ewha.ac.kr/ECgene/

631

EDAS

EST
-
derived alternative splicing database

http://ww
w.ig
-
msk.ru:8005/EDAS/

32

EID

Exon
-
intron database

http://www.meduohio.edu/bioinfo/eid/

34

ExInt

Exon

intron structure of eukaryotic genes

http://se
ge.ntu.edu.sg/wester/exint/

913

Extra
TRAIN

Extragenic regions and transcriptional regulators in bacteria and
archaea

http://www.era7.com/ExtraTrain/

782

FUGOID

Functional genomics of organelle introns data
base

http://web.austin.utexas.edu/fugoid/introndata/main.ht
m

970

H
-
DBAS

Human database of alternative splicing

http://jbirc.jbic.or.jp/h
-
dbas/

821

Hollywood

Exon annotation database

http://hollywood.mit.edu

36

HS
3
D

Homo Sapiens

Splice Sites Dataset

http://www.sci.unisannio.it/docenti/ra
mpone/

238

Intronerator

Alternative splicing in
C. elegans

and
C. briggsae

http://hgwdev
-
hiram.cse.ucsc.edu/IntronWS120/

1122

ProSAS

Protein Structure and Alternative Splicing: effects of alt
ernative
splicing events on protein structure

http://services.bio.ifi.lmu.de/ProSAS

46

SpliceDB

Canonical and non
-
canonical mammalian splice sites

http://www.softberry.com/berry.phtml?topic=splicedb&
group=data&subgroup=spldb

746

SpliceInfo

Modes of alternative splicing in human genome

http://spliceinfo.mbc.nctu
.edu.tw/

580

SpliceNest

Visualizing Splicing of Genes from EST Data

http://splicenest.molgen.mpg.de/

927

TassDB

TAndem Splice Site Database

http://helios.informatik.uni
-
freiburg.de/TassDB/

937

U12DB

Datab
ase of orthologous U12
-
type spliceosomal introns

http://genome.imim.es/cgi
-
bin/u12db/u12db.cgi

305

Xpro

Eukaryotic protein
-
enc
oding DNA sequences, both intron
-
containing and intron
-
less genes

http://origin.bic.nus.edu.sg/xpro/

342

Yeast Intron Database

Ares lab database of splicesomal introns in S. cerevisiae

http://www.cse.ucsc.edu/research/compbio/yeast_intro
ns.html


1.4. Transcriptional regulator sites and transcription factors



795

ABS

Annotated regulatory binding sites from orthologous promoters

http://genome.imim.es/datasets/abs2005/

231

ACTIVITY

Functional DNA/RNA site activity

http://wwwmgs.bionet.nsc.ru/mgs/systems/activity
/

308

ASPD

Artificial selected proteins/peptides database

http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/

805

CisRed

Human regulatory DNA sequence motifs

http://w
ww.cisred.org/

1058

CMGSDB

Computational models for gene silencing in C. elegans

https://bioinformatics.cs.vt.edu/cmgs/CMGSDB/

1062

COXPRESdb

Coexpressed genes and networks in human and mouse

http://coxpresdb.hgc.jp/

1063

CTCF Binding Site
DB

Experimentally identified and predicted CTCF binding sties

http://insulatordb.utmem.edu/

807

DBD

Transcription fac
tor prediction database

http://www.transcriptionfactor.org/

31

DBTBS

Bacillus subtilis

promoters and transcription factors

http://dbtbs.hgc.jp/

591

DBTSS

Database o
f transcriptional start sites

http://dbtss.hgc.jp/

663

DoOP

Databases of Orthologous Promoters: chordates and plants

http://doop.abc.hu/

106

DPInteract

Binding sites for E. coli DNA
-
binding proteins

http://arep.med.harvard.edu/dpinteract/

33

EPD

Eukaryotic promoter database

http://www.epd.isb
-
sib.ch/

329

GeneNet

Database on gene netw
ork components

http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet/

1036

GenomeTraFaC

Conserved regulatory elements of human and mouse genes

http://genometr
afac.cchmc.org

823

HTPSELEX

Transcription factor binding site sequences obtained using high
-
http://www.isrec.isb
-
sib.ch/htpselex/

throughput SELEX method

516

JASPAR

PSSMs for transcription factor DNA
-
binding sites

http://jaspar.cgb.ki.se

700

MAPPER

Putative transcription factor binding sites in various genomes

http://bio.chip.org/mapper

842

MPromDB

Mammalian promoter database

http://bioinformatics.med.ohio
-
state.edu/MPromDb

846

ODB

Operon database

http://odb.kuicr.kyoto
-
u.ac.jp/

185

ooTFD

Object
-
oriented transcription factors database

http://www.ifti.org/ootfd

1107

ORegAnno

Open REGulatory ANNOtation database

http://www.oreganno.org/

711

Osteo
-
Promoter
DB

Genes in osteogenic proliferation and differentiation

http://www.opd.tau.ac.il

40

PLACE

Plant cis
-
acting regulatory DNA elements

http://www.dna.affrc.go.jp/PLACE/

41

PlantCARE

Plant promoters and cis
-
acting regulatory elements

http://bioinformatics.psb.ugent.be/webtools/plantcare/h
tml/

563

PlantProm

Plant promoter sequences for RNA polymerase II

http://mendel.cs.rhul.ac.uk/mendel.php?topic=plantpro
m

1117

PlantTFDB

Plant Transcription Factor Database

http://planttfdb.cbi.pku.edu.cn

1005

PReMod

Predicted transcriptional regulatory modules

in the human genome

http://genomequebec.mcgill.ca/PReMod

566

PRODORIC

Prokaryotic database of gene regulation networks

http://prodoric.tu
-
bs.de/

42

PromEC

E.
coli promoters with experimentally
-
identified transcriptional start
sites

http://margalit.huji.ac.il/promec/

1123

ProTISA

Translation Initiation Site Annotation in prokaryotic genomes

http://mech.ctb.pku.edu.cn/protisa/

116

RegulonDB

Transcriptional regulation and operon organization in E.coli

http://regulondb.ccg.unam.mx/

45

rSNP Guide

SNPs in regulatory ge
ne regions

http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/

577

SCPD

Saccharomyces cerevisiae promoter database

http://rulai.cshl.edu/SCPD/

246

SELEXd
b

Selected DNA/RNA functional site sequences

http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/

1015

SwissRegulon
database

Genome
-
wide annotations of regulatory sites in the intergenic
regions

http://www.swissregulon.unibas.ch

227

TESS

Transcription element search system

http://www.cbil.upenn.edu/tess

904

TiProD

Tissue
-
specific promoter database

http://tiprod.cbi.pku.edu.cn:8080/index.html

756

Tractor_DB

Transcription factors in gamma
-
proteobacteria database

http://www.tractor.lncc.br

345

TRANS
Compel
®

Transcriptional regulation, composite regulatory elements

http://www.gene
-
regulation.com/pub/
databases.html#transcompel

340

TRANSFAC
®

Transcription factors, gene regu
lation, positional weight matrices

http://www.gene
-
regulation.com

1141

TransfactomeDB

Nucleotide sequence specificity and condition
-
specific regulatory
activity of trans
-
acting factors

http://bussemakerlab.org/YeastTransfactomeDB/

341

TRANSPATH

Signal transduction pathways, vizualization and expression data
analysis


http://www.bio
base.de/pages/products/databases.html

48

Transterm

Codon usage, start and stop signals

http://guinevere.otago.ac.nz/transterm.html

757

TRED

Transcriptional regulatory element database

http://r
ulai.cshl.edu/tred

49

TRRD

Transcription regulatory regions of eukaryotic genes

http://www.bionet.nsc.ru/trrd/

314

TrSDB

Transcription factor database

http://bioinf.uab.es/cgi
-
bin/trsdb/trsdb.pl

792

YEASTRACT

Yeast transcriptional regulation

http://www.yeastract.com


2. RNA
S
equence,
S
tructure and
F
unctions



229

16S and 23S
r
RNA
Mutation Database

16S and
23S ribosomal RNA mutations

http://ribosome.fandm.edu

1041

3D rRNA modification
maps

Locations of modified rRNA nucleotides within the 3D structure of
the ribosome

http://people.biochem.umass.edu/fournierlab/3dmodm
ap/

230

5S rRNA Database

5S rRNA sequences

http://biobases.ibch.poznan.pl/5SData/

411

Aptamer Database

Small RNA/DNA m
olecules binding nucleic acids, proteins

http://aptamer.icmb.utexas.edu

232

ARED


AU
-
rich element
-
containing mRNAs

http://brp.kfshrc.edu.sa/ARED

797

Argonaute

Gene regulation by mammalian microRNAs

http://argonaute.uni
-
hd.de

984

dbRES

D
atabase of known RNA editing sites

http://bioinfo.au.tsinghua.edu.cn/dbRES/

463

European rRNA
DB

All complete or nearly complete rRNA sequences

http://www.psb.ugent.be/rRNA/

1027

fRNAdb

Functional RNA Database: noncoding transcripts that affect gene
expression

http://www.ncrna.org/

878

Greengenes

Multiple sequence alignment of prokaryotic 16S rDNA

http://greengenes.llnl.gov/16S/

820

GRSDB

G
-
rich sequences database

http://bioinformatics.ramapo.edu/GRSDB2/

490

G
-
tRNA
-
db

Genomic tRNA Database

http://lowelab.ucsc.edu/GtRNAdb/

236

Guide RNA Database


No longer maintained

76

HIV Sequence
DB

HIV RNA
sequences

http://hiv
-
web.lanl.gov/

689

HuSiDa

Human siRNA database

http://itb.biologie.hu
-
berlin.de/~nebulus/sirna/index.htm

237

HyPaLib

Hybrid pattern library: structural elements in classes of RNA

Not actively
maintained

379

IRESdb
-

the Internal Ribosome Entry Site database

http://ifr31w3.toulouse.inserm.fr/IRESdatabase/

831

IRESite

Experimentally studied internal ribosome entry sites

http://www.iresite.org

838

MeRNA

Metal ion binding sites in RNA

http://merna.lbl.gov

1097

microRNA.org

microRNA target predictions and expression profiles

http://www.microrna.org

529

miRBase

MicroRNA sequences, names, and predicted targets in animals

http://microrna.sanger.ac.uk/sequences/

1098

miRGator

microRNA target prediction, functiona
l analysis, and gene
expression data

http://genome.ewha.ac.kr/miRGator/miRGator.html

994

miRGen

Animal microRNAs located in introns, exons, UTRs, pseudogenes
and CpG islands

http://www.diana.pcbi.upenn.edu/miRGen

895

miRNAMap

microRNA precursors and their mapping to targets in vertebrate
genomes

http://mirnamap.mbc.nctu.edu.tw

378

Mobile g
roup II introns

Database for mobile group II introns


http://www.fp.ucalgary.ca/group2introns/

840

MODOMICS

D
atabase of RNA modification pathways

http:/
/genesilico.pl/modomics/

997

NATsDB

Natural Antisense Transcripts database

http://nats.cbi.pku.edu.cn

380

NCIR

Non
-
Canonical Interactions in RNA

http://prion.b
chs.uh.edu/bp_type/

381

ncRNAs database

Non
-
coding RNAs with regulatory functions

http://biobases.ibch.poznan.pl/ncRNA/

705

NONCODE

D
atabase of noncoding RNAs

http://bioinfo.ibp.ac.cn/NONCODE/index.htm

845

NPInter

Noncoding RNA
-
protein interactions

http://bioinfo.ibp.ac.cn/NPInter/index.php

1114

piRNABank

Sequences and properties of
Piwi
-
interacting RNAs (piRNAs) in
human, mouse and rat

http://pirnabank.ibab.ac.in/

564

Plant snoRNA DB

snoRNA genes in plant species

http:
//bioinf.scri.sari.ac.uk/cgi
-
bin/plant_snorna/home

240

PLANTncRNAs


No longer maintained

241

PLMItRNA

Mitochondrial tRNA genes in photosynthetic eukaryotes

http://bighost.area.ba.cnr.it/PLMItRNA/

723

PolyA_DB

D
atabase of mammalian mRNA polyadenylation

http://polya.umdnj.edu/

242

PseudoBase

Database of RNA pseudoknots

http://wwwbio.leidenuniv.nl/~
Batenburg/PKB.html

1009

REDIdb

An RNA editing database

http://biologia.unical.it/py_script/search.html

382

Rfam

Non
-
coding RNA families

http://www.sanger.ac.uk/Software/Rfam/

243

RDP
-
II

Ribosomal Database Project

http://rdp.cme.msu.edu

244

RISSC

Ribosomal Internal Spacer Sequence Collection

http://egg.umh.e
s/rissc

245

RNA Modification
DB

Naturally modified nucleosides in RNA

http://medlib.med.utah.edu/RNAmods/

900

RNA SSTRAND

RNA secondary structure data and structural motifs

http://www.rnasoft.ca/sstrand

630

RNAdb

Mammalian noncoding RNA database

http://ncrna.bioinformatics.com.au

862

RNAi codex

Clones from mouse, human and rat shRNA libraries

http://codex.cshl.org

1162

siRecords

Experimentally tested mammalian siRNAs

http://sirecords.umn.edu/siRecords/

629

siRNAdb

Functional human siRNA sequences

http://sirna.cgb.ki.se

247

Small RNA Database


No longer maintained

869

snoRNA
-
LBME
-
db

Human snoRNAs and Cajal body
-
specific RNAs (scaRNAs)

http://www
-
snorna.biotoul.f
r/

962

Sno/scaRNAbase

Small nucleolar RNAs and cajal body
-
specific RNAs

http://gene.fudan.sh.cn/snoRNAbase.nsf

248

SRPDB

Signal recognition particle database

http://rnp.uthct.edu/rnp/SRPDB/SRPDB.html

383

Subviral RNA D
B

Database of viroids and viroid
-
like RNAs


http://subviral.med.uottawa.ca/

754

The Small Subunit
rRNA Modification
DB

Modified

nucleosides in small subunit rRNA


http://library.med.utah.edu/SSUmods/

250

tmRDB

tmRNA database

http://rnp.uthct.edu/rnp/tmRDB/tmRDB.html

249

tmRNA Website

tmRNA sequences and alignments

http://www.indiana.edu/~tmrna

251

tRNA Sequences


Has

not been updated

1148

Vir
-
Mir db

Pred
iction of viral microRNA candidate hairpins

http://alk.ibms.sinica.edu.tw

254

Yeast snoRNA
Database

Yeast small nucleolar RNAs

http://www.bio.umass.edu/biochem/rna
-
sequence/Yeast_snoRNA_Database/snoRNA_DataBa
se.html


3. Protein
S
equence
D
atabases




3.1. General sequence databases



163

EXProt

Sequences of proteins with experimentally verified function

http://www.cmbi.kun.nl/EXProt/

88

MIPS resources

Munich Information Center for Protein Sequences

databases

http://mips.gsf.de/

542

NCBI Protein database

All protein sequen
ces: translated from GenBank and imported
from other protein databases

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Prot
ein

714

PA
-
GOSUB

Protein sequences from model organisms, G
O assignment and
http://www.cs.ualberta.ca/~bioinfo/PA/

subcellular localization

194

PIR

Protein Information Resource

http://pir.georgetown.edu

565

PRF

Pr
otein research foundation database of peptides

http://www.prf.or.jp/en/index.shtml

790

TCDB

Transporter protein classification database

http://www.tcdb.org/

775

UniParc

UniProt archive, a repository of all protein seq
uences

http://www.uniprot.org/database/archive.shtml

318

UniProt

Universal Protein knowledgebase, combined information from
Swiss
-
Prot, TrEMBL, and PIR

h
ttp://www.uniprot.org

197

UniProtKB
\
Swiss
-
Prot

Formerly SwissProt, part of the UniProt knowledgebase

http://www.expasy.org/sprot

198

UniProtKB
\
TrEMBL

Now UniProt/TrEMBL, part of the UniProt knowledgebase

http://www.uniprot.org/database/knowledgebase.shtml

776

UniRef

Clustered sets of related sequences from UniProt

http://www.uniprot.org
/database/nref.shtml

1165

UniSave

UniProtKB Sequence/Annotation Version Archive

http://www.ebi.ac.uk/uniprot/unisave/


3.2. Protein properties



221

AAindex

Physicochemical properties of amino acid
s

http://www.genome.ad.jp/aaindex/

979

BindingDB

Binding affinities of protein
-
ligand and other complexes

http://www.bindingdb.org/bind/index.jsp

806

CyBase

Proteins with cyclic backbones

http://research1t.imb.uq.edu.au/cybase

885

dbPTM

Information on post
-
translational modification of proteins

http://
dbptm.mbc.nctu.edu.tw/

914

iProLINK

Annotated literature sources for protein features and names

http://pir.georgetown.edu/iprolink

1093

MALISAM

Manual alignments for structurally analogous motifs in proteins

http://prodata.swmed.edu/malisam

1094

MegaMotifbase

Structural motifs in protein families and superfamilies

http://caps.ncbs.res.in/MegaMotifbase/index.html

954

PIDD

Protein inter
-
atomi
c distances database

http://pidd.math.iastate.edu

854

PINT

Protein
-
protein interactions thermodynamic database

http://pintdb.dyndns.org/index.html

856

PPD

Experimentally
-
determined protein pKa values

http://www.jenner.ac.uk/ppd/

1120

PPT
-
DB

Protein Property Prediction and Testing Database

http://redpoll.pharmacy.ualberta.ca/PPT_DB/public_ht
ml/PPT_main.html

280

ProTherm

Thermodynamic data for wild
-
type and mutant proteins

http://gibk26.bse.kyutech.ac.jp/j
ouhou/protherm/prothe
rm.html

1176

PRTAD

Protein residue torsion angle database

http://www.math.iastate.edu/prtad

783

REFOLD

Experimental data on protein refolding and purification

http://refold.med.monash.edu.au


3.3. Protein localization and targeting



444

DBSubLoc
-

Database of protein Subcellular Localization

http://www.bioinfo.tsinghua.e
du.cn/dbsubloc.html

930

eSLDB

eukaryotic proteins Subcellular Localization Database

http://gpcr.biocomp.unibo.it/esldb

1021

InterFil

Human Intermediate Filament database

http://www.interfil.org

836

LOCATE

Subc
ellular localization of mouse proteins

http://locate.imb.uq.edu.au/

1022

MiCroKit

Midbody, Centrosome and Kinetochore proteins

http://bioinformatics.l
cd
-
ustc.org/microkit/

226

MitoDrome

Nuclear
-
encoded mitochondrial proteins of
Drosophila

http://www2.ba.itb.cnr.it/MitoDrome/

85

MitoRes

Nuclear genes coding for mitochondrial proteins

http://www2.ba.itb.cnr.it/MitoNuc/

375

NESbase

Nuclear export signals database

http://www.cbs.dtu.dk/databases/NESbase

376

NLSdb

Nuclear localization signals

http://cubic.bioc.columbia.edu/db/NLSdb/

704

NMPdb

Nuclear matrix associated proteins database

http://www.rostlab.org/db/NMPdb/

706

NOPdb:

Nucleolar p
roteome database

http://www.lamondlab.com/NOPdb/

369

NPD

Nuclear Protein Database

http://npd.hgu.mrc.ac.uk

182

Nuclear Receptor
Resource

Nuclear receptor superfamily

http://nrr.georgetown.edu/NRR/nrrhome.htm

183

NUREBASE

Nuclear hormone receptors database

http://www.ens
-
lyon.fr/LBMC/laudet/nurebase/nurebase.html

789

NURSA

Nuclear r
eceptor signaling atlas

http://www.nursa.org

734

PSORTdb

Protein subcellular localization in bacteria

http://db.psort.org/

745

Secreted Protein
DB

Secreted proteins from human, mo
use and rat

http://spd.cbi.pku.edu.cn

1014

SUBA

Subcellular localisation of
Arabidopsis

proteins

http://www.suba.bcs.uwa.edu.au/

587

THGS

Transmembrane Helices in

Genome Sequences

http://pranag.physics.iisc.ernet.in/thgs/

1140

TopDB

Topology Data Bank of transmembrane proteins

http://topdb.enzim.hu

589

Transmembrane
Protein Database


Transmembrane proteins with experimentally
-
characterized
transmembrane topologies

http://bioinfo.si.hirosaki
-
u.ac.jp/~TMPDB/


3.4. Protein sequence motifs and active sites



374

ASC

Active Sequence Collection

http://bioinformatica.isa.cnr.it/ASC/

203

Blocks

Alignments of conserved regions in protein families

http://blocks.fhcrc.org

4
38

COMe

Co
-
Ordination of Metals etc.

http://www.ebi.ac.uk/come/

771

CoPS

Comprehensive peptide signature database

http://cops.igib.res.in/copsv2/index.htm
l

440

CSA

Catalytic Site Atlas

http://www.ebi.ac.uk/thornton
-
srv/databases/CSA/

666

eBLOCKS

Highly conserved protein sequence blocks

http://fold.stanford.edu/eblocks/acsearch.html

452

eF
-
site

Electrostatic surface of Functional site

http://ef
-
site.protein.osaka
-
u.ac.jp/eF
-
site

206

eMOTIF

Protein sequence motif dete
rmination and searches

http://motif.stanford.edu/emotif

986

FireDB

Functionally important residues in protein structures

http://firedb.bioinfo.cnio.es/

207

In
terPro

Integrated resource of protein families, domains and functional
sites

http://www.ebi.ac.uk/interpro

179

Metalloprotein Site
DB

Metal
-
binding sites in metalloproteins

http://metallo.scripps.edu/

209

O
-
GLYCBASE

O
-

and C
-
linked glycosylation sites in proteins

http://www.cbs.dtu.dk/databases/OGLYCBASE/

717

PDBSite

3D structure of protein functional sites

http://srs6.bionet.nsc.ru/srs6bin/cgi
-
bin/wgetz?
-
page+LibInfo+
-
newId+
-
lib+PDBSite

187

Phospho.ELM

S/T/Y protein phosphorylation sites (former PhosphoBase)

http://phospho.elm.eu.org/

1003

Phospho3D

3D structures
of protein phosphorylation sites

http://cbm.bio.uniroma2.it/p3d/

212

PRINTS

Hierarchical gene family fingerprints

http://umber.sbs.man.ac.uk/dbbrow
ser/PRINTS/

193

PROMISE

Prosthetic centers and metal ions in protein active sites

http://metallo.scripps.edu/PROMISE/

899

ProRule

Functional and structural information on PROSITE profiles

http://www.expasy.org/prosite/prorule.html

215

PROSITE

Biologically
-
significant protein patterns and profiles

http://www.expasy.org/prosite

732

ProTeus

Signature
sequences at the protein N
-

and C
-
termini

http://www.proteus.cs.huji.ac.il

868

SitesBase

Known ligand binding sites in the PDB

http://www.modelling.leeds.ac.uk/sb/


3.5. Protein domain databases; protein
classification



622

ADDA

Datab
ase of protein domain classification

http://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb

288

BAliBASE

Benchmark database for comparison of multiple sequence
alignments


http://www
-
igbmc.u
-
strasbg.fr/BioInfo/BAliBASE2/index.html

978

Benchmark

Protein classification benchmark collection: training/test sets for
machine learning

http://net.icgeb.org/benchm
ark/

786

BIOZON

Datab
ase of gene and protein familiy classification

http://biozon.org

204

CDD

Conserved domain database, includes protein domains from Pfam,
SMART, COG and KOG databases

http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

205

CluSTr

Clusters of UniProt Knowledgebase and IPI proteins

http://www.ebi.ac.uk/clustr/

7

COG

Clusters of orthologou
s groups of proteins

http://www.ncbi.nlm.nih.gov/COG

448

DomIns


Database of Domain Insertions

http://www.domins.org/

1068

eggNOG

Evolutionary genealogy of genes: Non
-
supervised Orthologous
Groups

http://eggnog.embl.de

1069

EPGD

Eukaryotic Paralog Group Database

http://epgd.biosino.org:8080/EPGD/

963

EVEREST

Automatically generat
ed protein domain families

http://www.everest.cs.huji.ac.il

671

FunShift

Functional divergence between the subfamilies of a protein
domain family

http://FunShift.c
gb.ki.se

470

FusionDB

Database of bacterial and archaeal gene fusion events

http://www.igs.cnrs
-
mrs.fr/FusionDB/

200

Hits

Datab
ase of protein domains and motifs

http://hits.isb
-
sib.ch

266

HSSP

Homology
-
derived structures of proteins

http://srs.ebi.ac.uk/srsbin/cgi
-
bin/wgetz?
-
page+LibInfo+
-
lib+HSSP


510

InterDom

Putative protein
domain interactions

http://interdom.i2r.a
-
star.edu.sg/

208

iProClass

Integrated protein classification database

http://pir.georgetown.edu/iproclass/

844

MulPSSM

Multiple PSSMs of structural and sequen
ce families

http://hodgkin.mbu.iisc.ernet.in/~mulpssm

1109

PairsDB

Pairwise alignments of all sequences in UniProt

http://pairsdb.csc.fi

274

PALI

Phylogeny a
nd alignment of homologous protein structures

http://pauling.mbu.iisc.ernet.in/~pali

552

PANTHER

Protein sequence evolution mapped to functions and pathways

ht
tp://www.pantherdb.org

210

Pfam

Protein families: Multiple sequence alignments and profile hidden
Markov models of protein domains

http://pfam.sanger.ac.uk/

981

PhyloFacts

Phylogenomic analysis of protein families

http://phylogenomics.berkeley.edu/phylofacts/

561

PIRSF

Family/superfamily classification of whole proteins

http://pir.georgetown.edu/pirsf/

214

ProDom

Protein domain families

http:/
/prodom.prabi.fr/

216

ProtoMap

Hierarchical classification of Swiss
-
Prot proteins

http://protomap.cornell.edu

567

ProtoNet

Hierarchical clustering of Swiss
-
Prot proteins

http://www.protonet.cs.huji.ac.il/

217

SBASE

Protein domain sequences and tools

http://www.icgeb.org/sbase

867

SIMAP

Similarity matrix of proteins: precomputed similarity data

http://mips.gsf.de/sima
p/

1010

SISYPHUS

Structural alignments for proteins with non
-
trivial relationships

http://sisyphus.mrc
-
cpe.cam.ac.uk

218

SMART

Simple modular architecture research tool: signalling, extracellular
http://smart.embl
-
heidelberg.de

and ch
romatin
-
associated protein domains

219

SUPFAM

Grouping of sequence families into superfamilies

http://pauling.mbu.iis
c.ernet.in/~supfam

199

TIGRFAMs

TIGR

protein
fam
ilies adapted for functional annotation

http://www.tigr.org/TIGRFAMs






3.6. Databases of individual protein families



157

ABCdb

Archaeal and bacterial AB
C transporter database

http://www
-
abcdb.biotoul.fr

156

Aminoacyl
-
tRNA
synthetases database

A
mino
a
cyl
-
t
R
NA
s
ynthetase
d
ata
b
ase

http://rose.man.poznan.pl
/aars/index.html


1045

Animal Toxin D
B

Database of animal toxins

http://protchem.hunnu.edu.cn/toxin

412

ARAMEMNON

Arabidopsis

thaliana

membrane proteins and transporters

http://aramemnon.botanik.uni
-
koeln.de

1166

BACTIBASE

Database of bacteriocin natural antimicrobial peptides

http://www.pfba
-
lab.org/bactibase

158

BacTregulators

Transcriptional r
egulators of AraC and TetR families

No longer maintained

976

BANMOKI

Datab
ase of bacterial nucleoside monophosphate kinases

http://www.ces.clemson.edu/compbio/databases/kinas
es

1057

Chr
omDB

Chromatin
-
associated proteins in a broad range of organisms

http://www.chromdb.org

923

cpnDB

Chaperonin database

http://cpndb.cbr.nrc.ca/

1154

CREMOFAC

Datab
ase of chro
matin remodeling factors

http://www.jncasr.ac.in/cremofac/

364

CSDBase

Cold Shock Domain database

http://www.chemie.uni
-
marburg.de/~csdbase/

116
8

CyMoBase

Cytoskeletal and motor proteins database

http://www.motorprotein.de/cymobase

1065

DB
-
PABP

Experimentally characterized polyanion
-
binding proteins

http://ppa.bcf.ku.edu/DB_PABP/

658

DCCP

Database of Copper
-
Chelating Proteins

http://sdbi.sdut.edu.cn/DCCP/en/index.php

945

Defensins
Knowledgebase

Antimicrobial peptides of the defensin family

http:/
/defensins.bii.a
-
star.edu.sg/

160

DExH/D Family
DB

DEAD
-
box, DEAH
-
box and DExH
-
box proteins

http://www.helicase.net/dexhd/dbhome.htm

892

DSD

Datab
ase of dehydrogenase stereospecificities

http://ww
w.jenner.ac.uk/DSD

161

Endogenous GPCR List

G protein
-
coupled receptors; expression in cell lines

http://www.tumor
-
gene.org/GPCR/gpcr.html

814

EROP
-
Moscow

Datab
ase of Endogenous Regulatory OligoPep
tides

http://erop.inbi.ras.ru

162

ESTHER

Esterases and other alpha/beta hydrolase enzymes

http://bioweb.ensam.inra.fr/ESTHER/general?what=in
dex

164

FUNPEP

Low
-
complexity peptides capable of forming amyloid plaque

http://www.cmbi.kun.nl/swift/FUNPEP/gergo/

166

GPCRDB

G protein
-
coupled receptors database

http://www.gpcr.org/7tm/

679

gpDB

G
-
protein database: G
-
proteins and their interaction with GPCRs

http://bioinformatics.biol.uoa.gr/gpDB

1085

Heme Protein
DB

Heme protein structure, heme type
, axial ligands, and heme
protein reduction potential (Em) values

http://heme.chem.columbia.edu/heme.php

167

Histone Database

Histone fold sequences and structures

http://research.nhgri.nih.gov/histones/

365

HIV RT and Protease
Sequence Database

HIV reverse transcriptase and protease sequences

http://hivdb.stanford.edu

169

Homeobox Page

H
omeobox protei
ns, classification, and evolution

http://www.biosci.ki.se/groups/tbu/homeo.html

170

Homeodomain
Homeodomain sequences, structures, and related genetic and
http://research.nhgri.nih.gov/homeodomain/

Resource

genomic information

174

InBase

Inteins (protein splicing elements) database: properties,
sequences, bibliography

http://www.neb.com
/neb/inteins.html

518

KinG

Kinases in Genomes: Ser/Thr/Tyr kinases encoded in the
completely sequenced genomes

http://hodgkin.mbu.iisc.ernet.in/~king

519

Knottin database

Database of knottins, smal
l proteins with an unusual "disulfide
through disulfide" knot

http://knottin.cbs.cnrs.fr/

176

LGICdb

Ligand
-
gated ion channel subunit sequences database

http://www.pasteur.fr/recherche/banques/LGIC/LGIC.h
tml

368

Lipase Engineering DB

Sequence, structure and function of lipases and esterases

http://www.led.uni
-
stuttgart.de/

524

LOX
-
DB

Mammalian
, invertebrate, plant and fungal lipoxygenases

http://www.dkfz
-
heidelberg.de/spec/lox
-
db/

177

MEROPS

Database of proteolytic enzymes (peptidases)

http://
merops.sanger.ac.uk/

1105

NORINE

Datab
ase of nonribosomal peptides

http://bioinfo.lifl.fr/norine/

546

NucleaRDB

Nuclear receptor superfamily

http://www.receptors
.org/NR/

184

Olfactory Receptor DB

Sequences for olfactory receptor
-
like molecules

http://senselab.med.yale.edu/senselab/ordb/

186

Peptaibol

Peptaibol (antibiotic peptide) sequences

http://www.cryst.bbk.ac.uk/peptaibol/

560

PhytoProt

Clusters of (predicted) plant proteins

http://urgi.versailles.inra.fr/phytoprot/

189

PLANT
-
PIs

Plant
protease inhibitors

http://bighost.area.ba.cnr.it/PLANT
-
Pis

371

PlantsP/PlantsT

Plant proteins involved in phosphorylation and transport

http://plantsp.sdsc.ed
u

759

PLPMDB

Pyridoxal
-
5'
-
phosphate dependent enzymes mutations

http://www.studiofmp.com/plpmdb/

609

ProLysED

Datab
ase of bacterial protease systems

http://ge
nome.ukm.my/prolyses/

192

Prolysis

Proteases and natural and synthetic protease inhibitors

http://delphi.phys.univ
-
tours.fr/Prolysis/

188

Protein kinase resource

Protein kinase resource: sequenc
es, enzymology, genetics and
molecular and structural properties

http://www.kinasenet.org/pkr/

224

REBASE

Restriction enzymes and associated methylases

h
ttp://rebase.neb.com/rebase/rebase.html

195

RNAse P Database

Ribonuclease P sequences, alignments and structures

http://www.mbio.ncsu.edu/RNaseP/home.html

901

RNRdb

Ribonucleotide reductase datab
ase

http://rnrdb.molbio.su.se/

573

RPG

Ribosomal Protein Gene database

http://ribosome.miyazaki
-
med.
ac.jp/

575

RTKdb

Receptor Tyrosine Kinase database

http://pbil.univ
-
lyon1.fr/RTKdb/

372

SDAP

Structural database of allergenic proteins and food allergens

http
://fermi.utmb.edu/SDAP

1131

SelenoDB

Datab
ase of selenoprotein genes, proteins and SECIS elements

http://www.selenodb.org/

196

SENTRA

Sensory signal transduction proteins

http://compbio.mcs.anl.gov/sentra/

373

SEVENS

7
-
transmembrane helix receptors (G
-
protein
-
coupled)

http://sevens.cbrc.jp/1.20/

1137

Telomerase database

Sequences and structures of the RNA and protein s
ubunits of
telomerase, mutations of telomerase components

http://telomerase.asu.edu

311

TransportDB

Predicted membrane transporters in complete genomes, classified
according to the TC classification system

http://www.membranetransport.org

399

VKCDB

Voltage
-
gated K
+

Channel Database

http://vkcdb.biology.ualberta.ca/

202

Wnt Database

Wnt proteins and phenotypes

http://www.stanford.edu/~rnusse/wntwindow.html


4. Structure Databases




4.1. Small molecules



402

AANT

Amino Acid
-

Nucleotide interaction database

http://aant.icmb.utexas.edu/

646

ChEBI

Chemical entities of biological interest

http://www.ebi.ac.uk/chebi/

1024

ChemBank

Structures and biological activities of small organic molecules

http://chembank.broad.harvard.edu/

1023

ChemDB

3D structures and properties of small molecules

http://cdb.ics.uci.edu

261

CSD

Cambridge Structural Database

http://www.ccdc.cam.ac.uk/prods/csd/csd.html

360

Het
-
PDB Navi

Hetero
-
atoms in protein structures

http://daisy.bio.nagoya
-
u.ac.jp/golab/hetpdbnavi.htm
l

265

HIC
-
Up

Hetero
-
compound Information Centre
-

Uppsala

http://xray.bmc.uu.se/hicup/

111

Klotho

Collection and categorization of biological compounds

http:/
/www.biocheminfo.org/klotho/

113

LIGAND

Chemical compounds and reactions in biological pathways

http://www.genome.ad.jp/ligand/

615

PDB
-
Ligand

3D structures of small molecules bound to proteins and nucleic

acids

http://www.idrtech.com/PDB
-
Ligand/

735

PubChem

Structures and biological activities of small organic molecules

http://pubchem.ncbi.nlm.nih.gov/

11
27

R.E.DD.B.

RESP and ESP atomic charges and force field libraries for small
molecules and molecular fragments

http://q4md
-
forcefieldtools.org/REDDB


4.2. Carbohydrates



977

BCSDB/Glycoscience

Bacter
ial Carbohydrate Structure DataBase

http://www.glyco.ac.ru/bcsdb/start.shtml

429

CarbBank

CCSD
-

Complex Carbohydrate Structure Database

http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm

652

CSS

Carbohydrate Structure Suite: carbohydrate 3D structures

http://www.dkfz.de/spec/css/

486

Glycan

Carbohydrate database, part of the KEGG sy
stem

http://glycan.genome.ad.jp/

1080

Glycoconjugate Data
Bank

Annotated structures of glycan molecules

http://daisy2.nagahama
-
i
-
bio.ac.jp/structures
/

988

GlycoMaps DB

Conformational maps of disaccharides

http://
www.glycosciences.de/modeling/glycomapsdb/

292

GlycoSuiteDB

N
-

and O
-
linked glycan structures and biological sources

http://www.glycosuite.com

535

Monosaccharide
Browser

Space filling Fischer projections of monosaccharides


http://www.terravivida.com/vivida/monosaccharid
e/

300

SWEET
-
DB

Annotated carbohydrate structure and substance information

http://www.dkfz
-
heidelberg.de/spec2/sweetdb/


4.3. Nucleic acid structure



1082

Greglist

G
-
quadruplex motifs and po
tentially G
-
quadruplex regulated genes

http://tubic.tju.edu.cn/greglist/

1090

ITS2

Predicted structures of internal transcribed spacer 2 (ITS2)
molecules

http://its2.bioapps.biozentrum.uni
-
wuerzburg.de/ITS2_db.html

272

NDB

Nucleic acid
-
containing structures

http://ndbserver.rutgers.edu/

273

NTDB

Thermodynamic data for nucleic acids

http://ntdb.chem.cuhk.edu.hk

1126

QuadBase

G
-
quadruplex motifs in the promoters of human, chimpanzee, rat,
http://quadbase.igib.res.in/

mouse and bacterial genes

112
9

RNA FRABASE

Datab
ase of 3D RNA fragments within known RNA structures

http://rnafrabase.ibch.poznan.pl/

387

RNABase

RNA
-
containing structures from PDB and NDB

http:/
/www.rnabase.org

1130

RNAJunction

RNA structural elements: helical junctions, internal loops, bulges
and loop
-
loop interactions

http://rnajunction.abcc.ncifcrf.gov

908

SARS
-
CoV RNA SSS

Predicted secon
dary structures of SARS coronavirus RNA

http://www.liuweibo.com/sarsdb/

283

SCOR

S
tructural
c
lassification
o
f
R
NA: RNA motifs by structure, function

and tertiary interactions

http://scor.lbl.gov


4.4. Protein structure



401

3D
-
Genomics

Structural annotations for complete proteomes

http://www.sbg.bio.ic.ac.uk
/3dgenomics

633

3DID

3D interacting domains

http://gatealoy.pcb.ub.es/3did/

413

ArchDB

Automated classification of protein loop structures


http://gurion.imim.es/archdb

255

ASTRAL

Sequences of domains of kno
wn structure, selected subsets and
sequence
-
structure correspondences

http://astral.berkeley.edu/

1047

AutoPSI

Automated structural classification of protein sequences

http://www.bio.ifi.lmu.de/AutoPSIDB

257

BioMagResBank

NMR spectroscopic data from proteins, peptides, and nucleic acids


http://www.bmrb.wisc.edu/

384

CADB

Conformational Angles DataBase of Proteins

http://cluster.physics.iisc.ernet.in/cadb/

258

CATH

Protein domain structures database

http://www.cathdb.info/

259

CE

Combinatorial Extension method to compute

and review 3D
protein structure alignments

http://cl.sdsc.edu/ce.html

260

CKAAPs DB

Conserved Key Amino Acid Positions Database

No longer maintai
n
ed

882

CoC Central

Universally conserved residues in protein fol
ds

http://kulibin.mit.edu/coc/

1059

ColiSNP

Mapping non
-
synonymous SNPs on protein structures

http://yayoi.kansai.jaea.go.jp/colisnp

883

Columba

Annotation

of protein structures from the PDB

http://www.columba
-
db.de

442

Dali database

Fold classification based on structural alignment of proteins

http://e
khidna.biocenter.helsinki.fi/dali/start

1169

DBAli

Datab
ase of structure alignments

http://salilab.org/DBAli/

385

Decoys
-
R
-
Us

Computer
-
generated protein conformations based on sequence
data

http://dd.compbio.washington.edu/

447

DisProt

Database of Protein Disorder

http://divac.ist.temple.edu/disprot

809

DMAPS

Datab
ase of multiple alignments for protein structur
es

http://bioinformatics.albany.edu/~dmaps

264

DSDBASE

Disulfide Database

http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase
.
html

386

DSMM

A Database of Simulated Molecular Motions

http://projects.villa
-
bosch.de/dbase/dsmm/

456

E
-
MSD

EBI
-
Macromolecular Structure Database

http:
//www.ebi.ac.uk/msd

818

FSN

Flexible structural neighborhood, structural neighbors of proteins
identified by FATCAT tool

http://fatcat.ljcrf.edu/fatcat
-
cgi/cgi/stru
ct_neibor/fatcatStructNeibor.pl

469

FSSP


Superseded by the Dali database, no. 442

472

Gene3D

Precalculated structural assignments for whole genomes

http://cathwww.biochem.ucl.ac.uk:8080/Gene3
D/

489

Genomic Threading DB

Structural annotations of complete genomes

http://bioinf.cs.ucl.ac.uk/GTD

322

GTOP

Protein fold predictions from genome sequences

http://spock.genes.nig.ac.jp/~genome/gtop.html

498

HOMSTRAD

Homologous structure alignment database: curated structure
-
based alignments for protein families

http://www
-
cryst.bioc.cam.a
c.uk/homstrad

267

IMB Jena Image Library

Visualization and analysis of 3D biopolymer structures

http://www.imb
-
jena.de/IMAGE.html

502

IMGT/3Dstructure
-
DB

3D structures of Immunoglobulins, T cell receptor
s, and MHC
proteins

http://imgt3d.igh.cnrs.fr/

829

IMOTdb

Spatially interacting motifs in proteins

http://caps.ncbs.res.in/imotdb/

269

LPFC

Library of protein fam
ily core structures

http://helix
-
web.stanford.edu/LPFC/

270

MMDB

All experimentally
-
determined 3D structures, linked to NCBI Entrez

http://www.ncbi.n
lm.nih.gov/Structure/

331

ModBase

Annotated comparative protein structure models

http://salilab.org/modbase

262

MolMovDB

Database of Macromolecular Movements

http://bioinfo.mbb.yale.edu/MolMovDB/

107

MPID

MHC
-
Peptide Interaction Database

http://surya.bic.nus.edu.sg/mpidt

275

PASS2

Structural motifs of protein superfamilies

http://www.ncbs.res.in/~faculty/mini/campass/pass2.ht
ml

276

PDB

Protein Data Bank: all known protein structures

http://www.pdb.org/

619

PDB_TM

Transmembrane proteins with known 3D

structure

http://pdbtm.enzim.hu/

277

PDB
-
REPRDB

Representative protein chains, based on PDB entries

http://mbs.cbrc.jp/pdbreprdb
-
cgi/reprdb_menu.pl

2
78

PDBsum

Summaries and analyses of PDB structures

http://www.ebi.ac.uk/thornton
-
srv/databases/pdbsum/

557

PepConfDB

Datab
ase of peptide conformations

http://www.peptidome.org/products/list.htm

719

PFD

Protein Folding Database : Experimental data on protein folding

http://www.foldeomics.org/pfd/public_html/index.
php

855

PMDB

3D protein models obtained from structure predictions

http://www.caspur.it/PMDB/

281

RESID

Post
-
translational modifications of proteins

http://www.ebi.ac.
uk/RESID/

740

S4

Structure
-
based Sequence Alignments of SCOP Superfamilies

http://compbio.mds.qmw.ac.uk/~james/S4.shtml

282

SCOP

Structural classification of proteins

http://scop.mrc
-
lmb.cam.ac.uk/scop

863

SCOPPI

Structural classification of protein
-
protein interfaces

http://www.scoppi.org

284

SLoop

Classification of protein loops

http://www
-
cryst.bioc.cam.ac.uk/~sloop/

530

SSToSS

Sequence
-
Structural Templates of Single
-
member Superfamilies

http://caps.ncbs.res.in/SSTOSS/index.htm

785

STIN
G Report

Amino acid properties in proteins of known structure

http://sms.cbi.cnptia.embrapa.br/SMS/STINGm/SMSR
eport/

583

Structure Superposition
Database

Pairwise superpositions of 115

TIM
-
barrel structures

http://ssd.rbvi.ucsf.edu/

285

SUPERFAMILY

Assignments of proteins to structural superfamilies

http://supfam.org/SUPERFAMILY/

584

SURFACE

Surf
ace residues and functions annotated, compared and
evaluated: a database of protein surface patches

http://cbm.bio.uniroma2.it/surface

585

SWISS
-
MODEL
Repository

3D protein structure models generated by a
utomated homology
modeling using SWISS
-
MODEL

http://swissmodel.expasy.org/repository

764

TargetDB

Target data from worldwide structural genomics projects

http:
//targetdb.pdb.org/

938

TMBETA
-
GENOME

Beta
-
barrel membrane proteins encoded in various genomes

http://tmbeta
-
genome.cbrc.jp/annotation/

941

TOPOFIT
-
DB

Protein structural alignments based on the TO
POFIT method

http://mozart.bio.neu.edu/topofit/

310

TOPS

Topology Of Protein Structures

http://www.tops.leeds.ac.uk


5. Genomics Databases (non
-
human)




5
.1. Genome annotation terms, ontologies and nomenclature



915

BioThesaurus

A collection of gene/protein names and associated sequences

http://pir.georgetown.edu/iprolink/biothesaurus

1075

F
unSimMat

Gene Ontology
-
based functional similarity values for proteins and
protein families

http://gotax.bioinf.mpi
-
inf.mpg.de/funsimmat/

487

GO

Gene ontology consortium database

http://www.geneontology.org/

389

GOA

Gene Ontology Annotation

http://www.ebi.ac.uk/GOA

939

GOPaD

Gene Ontology Partition Database

http://bcl.med.harvard.edu/proj/gopart

73

HGNC Database

The HUGO Gene Nomenclature Database (formerly Genew)

http://www.genenames.org/

513

IUBMB Nomenclature
database

Nomenclature of enzymes, membrane transp
orters, electron
transport proteins and other proteins

http://www.chem.qmul.ac.uk/iubmb/

514

IUPAC Nomenclature
database

Nomenclature of biochemical and organic compounds approved
by the IUBMB
-
IUPAC Joint
Commission

http://www.chem.qmul.ac.uk/iupac/

515

IUPHAR
-
RD

International Union of Pharmacology recommendations on
receptor nomenclature and drug classification

http://www.iuphar
-
db.org/iuphar
-
rd/

926

Plant Ontology DB

Controlled vocabulary of plant structures and growth stages

http://www.plantontology.org

358

SOURCE

Functional genomics resource for human, mouse and rat

http://source.stanford.edu

906

TreeBase

Phylogenetic trees and the data matrices used to generate them

http://www.treebase.org/

317

UMLS

Unified medical language system

Requires user registration


5.2.

Taxonomy and identification



1018

GeneTrees

Pre
-
compiled alignments and gene phylogenies for a variety of
taxonomic groups

http://genetrees.vbi.vt.edu

78

ICB

gyrB

database for identification of bacteria

http://seasquirt.mbio.co.jp/icb/

1088

IDBD

Infectious Disease Biomarker Database

http://biomarker.korea.ac.kr

297

NCBI Taxonomy
Browser

Names of all organisms that

are represented in GenBank

http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhom
e.html

299

RIDOM

Ribosomal Differentiation of Medical Microorganisms

h
ttp://www.ridom.de/

1135

SuperCAT

Datab
ase for multilocus sequence typing analysis of the Bacillus
cereus group of bacteria

http://mlstoslo.uio.no/

301

Tree of Life

Information on phylogeny and biodiversity

http://phylogeny.arizona.edu/tree/phylogeny.html

965

VNTR Locus DB

Bacterial Variable Number Tandem Repeat locus database

http://vntr.csie.ntu.edu.tw/


5.3. General genomics databases



641

BacMap

Picture atlas of annotated bacterial genomes

http://wishart.biology.ualberta.ca/BacMap/

650

CoGenT++

Complete genome tracking: Predicted peptides fr
om fully
sequenced genomes

http://cgg.ebi.ac.uk/cgg/cpp_sitemap.html

445

DEG

Database of Essential Genes

http://tubic.tju.edu.cn/deg

1172

diArk

Datab
a
se of eukaryotic sequencing projects

http://www.diark.org/diark/

451

EBI Genomes

EBI’s collection of databases for the analysis of complete and
unfinished viral, pro
-

and eukaryotic genomes

http://www.ebi.ac.uk/genomes

458

Entrez Genomes

NCBI’s collection of databases for the analysis of complete and
unfinished viral, pro
-

and eukaryotic genomes

ht
tp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Ge
nome

461

ERGO
-
Light

Integrated biochemical data on 10 bacterial genomes: Publicly
-
available portion of the ERGO database

http://www.ergo
-
light.com/

674

GenDiS

Ge
nomic distribution of protein structural superfamilies

http://caps.ncbs.res.in/gendis/home.html

327

GeneNest

Gene indices of human, mouse, zebrafish, etc.

http://genenest.molgen.mpg.de/

1077

GenoList

An integrated environment for comparative analysis of microbial
genomes

http://genolist.pasteur.fr/

484

Genome Information
Broker

DDBJ’s collection of genome dat
abases

http://gib.genes.nig.ac.jp

678

Genome Reviews

Integrated view of complete genomes

http://www.ebi.ac.uk/GenomeReviews/

916

Genome Project DB

NCBI's dat
abase of large
-
scale genome sequencing projects

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=s
earch&DB=genomeprj

75

GOLD

Genomes online database: a listing of completed and ongoing
genome projects

http://
www.genomesonline.org/

830

HOINVGEN

Homologous invertebrate genes

http://pbil.univ
-
lyon1.fr/databases/hoinvgen/HOINVGEN.html

690

Inparanoid

Datab
ase of eukaryotic orthologs

http:
//inparanoid.cgb.ki.se/

223

Integr8

Functional classification of proteins in whole genomes

http://www.ebi.ac.uk/integr8/

777

KaryotypeDB

Karyotype and chromosome data for animal and plant species

http://www.nenno.it/karyotypedb/

112

KEGG

Kyoto Encyclopedia of Genes and Genomes: databases on genes,
proteins, and metabolic pathways

http://www.genome.ad.jp/kegg

528

MBG
D

Microbial genome database for comparative analysis

http://mbgd.genome.ad.jp/

114

MetaCyc

Metabolic pathways and enzymes from various organisms

http://metacyc.org/

1103

Narci
sse

Conserved syntenies for various animal, plant and bacterial
genomes

http://narcisse.toulouse.inra.fr

703

NegProt

Negative Proteome: A tool for comparison of complete proteomes

http://superfly.ucsd.edu/negprot

1040

NMPDR

Datab
ase for functional annotation and comparative analysis of
microbial genomes

http://www.nmpdr.org

1106

OPTIC

Orthologous and Paralogous Transcri
pts in Clades

http://genserv.anat.ox.ac.uk/

549

ORFanage

Orphan ORFs (ORFs with no homologs) in microbial genomes

No longer maintained

1108

OrthoDB

An hierarchical catalog of orthologous proteins in metazoa

http://cegg.unige.ch/orthodb/browse

847

OrthoMCL

Orthologous protein clusters from multiple genomes

http://orthomcl.cbil.upenn.edu

715

PartiGeneDB

Assembl
ed partial genomes for ~250 eukaryotic organisms

http://www.partigenedb.org/

354

PEDANT

Results of an automated analysis of genomic sequences

http://pedant.gsf.de

377

PEP


Predictions for Entire Proteomes

http://cubic.bioc.columbia.edu/pep/

1113

PhylomeDB

Experimentally validated and predicted serine phosphorylation sites
in
Arabidopsis thaliana

http://phylomedb.bioin
fo.cipf.es

118

PUMA2

Metabolic analysis of complete microbial genomes

http://compbio.mcs.anl.gov/puma2/

582

STRING

Predicted functional associations between proteins

http://string.embl.de/

66

TIGR Comprehensive
Microbial Resource

Various data on complete microbial genomes: Uniform annotation,
properties of DNA and predicted proteins

http://www.tigr
.org/tigr
-
scripts/CMR2/CMRHomePage.spl

5

TIGR Gene Indices

Organism
-
specific databases of EST and gene sequences

http://www.tigr.org/tdb/tgi.shtml

99

TIGR Microbial DB

A list of microbial genome sequenci
ng projects

No longer maintained

877

VBI Microbial Database

Virginia Bioinformatics Institute microbial database

http://phytophthora.vbi.vt.edu


5.4. Viral genome databases



1051

BioHealthBase

Host
-
pathogen interactions of influenza virus

http://dev.biohealthbase.org/GSearch/PrototypeIndex
.jsp

1061

CoVDB

Database of coronavirus genes and genomes

http://covdb.microbiology.hku.hk

8
10

DPVweb

Descriptions of plant viruses

http://www.dpvweb.net

1034

euHCVdb

European Hepatitis C Virus database

http://euhcvdb.ibcp.fr

492

HCV Database

Hepatitis C Virus (HCV) Sequence Database

http://hcv.lanl.gov/

473

HCVdb

Hepatitis C Virus Database

http://hepatitis.ibcp.fr/

972

HepSeq

Epidemiological, clinical, and sequence data on the Hepatitis B
virus

http://www.hpa
-
bioinfodatabases.org.uk/
hepatitis_open/main.php

495

HERVd

Human Endogenous Retrovirus database

http://herv.img.cas.cz

497

HIV Drug Resistance
Data
base

HIV mutations that confer resistance to anti
-
HIV drugs

http://resdb.lanl.gov/Resist_DB/default.htm

168

HIV Molecular
Immunology Database

HIV epitopes

http://hiv
-
web.lanl.gov/immunology/

990

HIV Positive Selection
Mutation Database

Positively selected mutations in HIV
-
1 protease and reverse
transcriptase

http://bioinfo.mbi.ucla.edu/HIV

909

Inf
luenza Virus
Resource

Protein and nucleotide sequences of the influenza virus

http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html

993

IVDB

Influenza Virus Database : Annotated sequences and geographic
distribution of the influenza virus

http://influenza.genomics.org.cn

602

NCBI Viral Genomes

Viral genome resource at NCBI

http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/virus
es.html

725

Poxvi
rus.org

Poxvirus genomic sequences and gene annotation

http://www.poxvirus.org

750

T4
-
like genome DB

Sequences of T4
-
like bacteriophages from various sources

http://phage.bioc.tulane.edu

201

VIDA

Homologous
viral protein families database

http://www.biochem.ucl.ac.uk/bsm/virus_database/VI
DA.html

761

VIPERdb

Virus particle explorer: Virus capsid structures

http://viperdb.scripps.edu/

798

Viral Bioinformatics
Resource Center

Virus orthologous genes, gene families and genomes

http://www.biovirus.org

397

VirGen

Curated database for complete viral genome sequences

http://bioinfo.ernet.in/virgen/virgen.html

1039

ViTa

microRNAs targets of the influenza virus

http://vita.mbc.nctu.edu.tw


5.5. Prokaryotic genome databases




5.5.1. General



1044

AlterORF

Database of alternate open reading frames

http://www.cienciavida.cl/alterorf/

641

BacMap

Picture atlas of annotated bacterial genomes

ht
tp://wishart.biology.ualberta.ca/BacMap

884

Comparative
Genometrics

DNA walks, nucleotide skews and other biometric measures of
prokaryotic genomes

http://www.unil.ch/comparativegenometrics/

70

EMGlib

Enhanced microbial genomes library: Completely sequenced
genomes of unicellular organisms

http://pbil.univ
-
lyon1.fr/emglib/emglib.html

328

GeneDB

Curated database for various Sanger
-
seq
uenced genomes

http://www.genedb.org/

611

Genome Atlas

DNA structural properties of sequenced genomes

http://www.cbs.dtu.dk/services/GenomeAtlas/

1084

HEG
-
DB

Predicted highly expressed genes in prokaryotic genomes

http://genomes.urv.cat/HEG
-
DB

352

HGT
-
DB

Horizontal Gene Transfer
-
DataBase

http://www.fut.es/~debb/HGT/

828

IMG

Comparative analysis of microbial genomes sequenced

at the DOE
Joint Genome Institute

http://img.jgi.doe.gov/

1089

IMG/M

A data management and analysis system for metagenomes

http://img.jgi.doe.gov/m

826

Interrupted coding
sequences DB

Interrupted coding sequences:

frameshifts, stop codons,
sequencing errors in microbial genomes

http://www
-
bio3d
-
igbmc.u
-
strasbg.fr/ICDS/

837

MeGX

M
arine
e
cological
g
enomi
x
: genomics and
metagenomics of marine
bacteria

http://www.Megx.net

614

MetaGrowth

Growth requirements of bacterial pathogens

http://igs
-
server.cnrs
-
mrs.fr/axenic/

959

MiST

Microbial Signal Transduction database

http://genomics.ornl.gov/mist/

720

PGTdb

P
rokaryotic
g
rowth
t
emperature database

http://pgtdb.csie.ncu.edu.tw/

43

RRNDB

rRNA operon numbers in various prokaryotes

http://rrndb.cme.msu.edu

1160

Roundup

Repository of orthologs and corresponding evolutionary distances

http://rodeo.med.harvard.edu/tools/roundup

866

SID
DBase

Stress
-
induced DNA duplex destabilization profiles of complete
microbial genomes

http://www.genomecenter.ucdavis.edu/benham/siddb
ase/

426

xBase

A family of
group
-
specific
bacteria
l genome

databases
, includes
coliBASE, CampyDB, ClostriDB, MycoDB, PseudoDB and other
s

http://xbase.bham.ac.uk/


5.5.2.
Escherichia coli



415

ASAP

A Systematic Annotation Package

https://asap.ahabs.wisc.edu/annotation/php/ASAP1.h
tm

428

CCDB

CyberCell Database

http://redpoll.pharmacy.ualberta.ca/CCDB

436

coliBase

Datab
ase for
E. coli
,
Sa
lmonella

and
Shigella


http://colibase.bham.ac.uk/

437

Colibri


http://genolist.pasteur.fr/Colibri/

623

EchoBASE

Post
-
genomic studies of
Escherichia coli

http
://www.ecoli
-
york.org/

108

EcoCyc

E. coli

K12 genes, pathways, transporters, and gene regulation

http://ecocyc.org/

69

EcoGene

Sequence and literature data on
E. coli

genes and proteins

http://ecogene.org/

1070

ERIC

Enteropathogen Resource Integration Center

http://www.ericbrc.org

462

Essential genes in
E.
coli

A list of genes essential for viability of
E. coli


http://www.genome.wisc.edu/resources/essential.htm

482

GenoBase

Functional genomic aAnalysis of
E. coli

in Japan

http://ecoli.aist
-
nara.ac.jp/

165

GenProtEC

E. coli

K12 gen
ome and proteome database

http://genprotec.mbl.edu


5.5.3.
Bacillus subtilis




424

BSORF

Bacillus subtilis

Open Reading Frames

http://bacillus.genome.ad.jp/

31

DB
TBS

Bacillus subtilis

promoters and transcription factors

http://dbtbs.hgc.jp/

89

NRSub

Non
-
redundant
Bacillus subtilis

database at U. Lyon

http://pbil.univ
-
ly
on1.fr/nrsub/nrsub.html

96

SubtiList

Bacillus subtilis

genome database at Institut Pasteur

http://genolist.pasteur.fr/SubtiList/


5.5.4.
Other bacteria




1153

BuchneraBase

Genomic database for the
pea aphid symbiont
Buchnera

sp. APS

http://www.buchnera.org/

426

CampyDB

Campylobacter

Database

Incoroporated into xBase, no. 426

648

CIDB

Chlamydia

Interactive Database: Gene expression data

http://www.it.deakin.edu.au/CIDB

433

ClostriDB

Clostridium

Database

Incoroporated into xBase, no. 426

1167

CoryneRegNet

Corynebacterial transcription factors

http://www.corynereg
net.de

68

CyanoBase

Cyanobacterial genomes

http://www.kazusa.or.jp/cyano/

834

LEGER

Post
-
genome research of
Listeria

http://leger2.gbf.de/cgi
-
bin/exp
Leger.pl

521

LeptoList

Leptospira interrogans

genome

http://www.bioinfo.hku.hk/LeptoList/.

534

MolliGen

Genomic data on mollicutes

http://cbi.labri
.fr/outils/molligen/

896

MtbRegList

Mycobacterium tuberculosis

gene regulation

http://www.USherbrooke.ca/vers/MtbRegList

996

MvirDB

Protein toxins, virulence factors, and antibiotic resistance ge
nes

http://mvirdb.llnl.gov/

944

PAIDB

Pathogenicity islands in bacterial genomes

http://www.gem.re.kr/paidb

1000

PATRIC

PathoSystems Resource Integration Center

https://patric.vbi.vt.edu

555

PEC

Profiling of
E. coli

Chromosome

http://shigen.lab.nig.ac.jp/ecoli/pec

720

PGTdb

Prokaryotic growth temperature database

http://pgt
db.csie.ncu.edu.tw/

733

PseudoCAP

Pseudomonas aeruginosa

community genome annotation project

http://www.pseudomonas.com/

947

RegTransBase

Manually curated database of regulatory interactions in prokaryotes

http://regtransbase.lbl.gov

94

RsGDB

Rhodobacter sphaeroides

genome

http://www.hgsc.bcm.tmc.edu/projects/microbial/Rsph
aeroides/

865

Shi
Base

Shigella

database

http://www.mgc.ac.cn/ShiBASE/

760

VFDB

Virulence Factors of pathogenic bacteria

http://www.mgc.ac.cn/cgi
-
bin/VFs/compatho.cgi

1017

xanthusBase

Genome of the social bacterium
Myxococcus xanthus

http://www.xanthusbase.org/


5.5.5.
Archaea



964

Sulfolobus

Database

Comparative genomics of
Sulfolobus

species

http://www.sulfolobus.org

876

UCSC Archaeal
Genome Browser

Pyrococcus furiosus

genome browser

http://archaea.ucsc.edu/


5.6. Unicellular eukaryotes genome databases



969

ApiDB

Unified resource fo
r various apicomplexan species

http://ApiDB.org

409

ApiDots

EST sequences from various
Apicomplexan

parasites

http://www.cbil.upenn.edu/apidots/

983

Comparasite

Datab
ase

for comparative study of parasite cDNAs

http://comparasite.hgc.jp/

439

CryptoDB

Cryptosporidium

database

http://cryptodb.org/

662

Diatom EST DB

ESTs from diatom algae
Thalassiosira
and
Phaeodactylum

http://www.biolog
ie.ens.fr/diatomics/EST/

446

DictyBase

Universal resource for
Dictyostelium discoideum


http://dictybase.org/

72

Full
-
Malaria

Full
-
length cDNA library from erythrocytic
-
stage
Plasmodium

http://fullmal.ims.u
-
tokyo.ac.jp

917

ParameciumDB

Paramecium

genome sequencing project

http://paramecium.cgm.cnrs
-
gif.fr/db/index

91

PlasmoDB

Plasmodium

genome database

http://PlasmoDB.org

1124

ProtozoaDB

Comparative

analysis of
protozoan genomes

http://protozoa.biowebdb.org/

912

TBestDB

Taxonomically broad EST database: protist ESTs

http://tbestdb.bcm.umontreal.ca/

586

TcruziDB

Trypanosoma cruzi

genome database

http://tcruzidb.org/

359

ToxoDB

Toxoplasma gondii

genome database

http://ToxoDB.org

910

U
-
genome

Genome organization in unicellular eukaryotes

http://sege.ntu.edu.sg/wester/ugenome/


5.7. Fungi



1056

CFGP

Comparative Fungal Genomics Platform

http://cfgp.snu.ac.kr

955

Fungal Genome Size
Database

Genome sizes of various fungi

http://www.zbi.ee/fungal
-
genomesize/


5.7.1. Yeasts



635

AGD

Ashbya gossypii

genome databas
e

http://agd.unibas.ch

617

CandidaDB

Candida albicans
genome database

http://genolist.pasteur.fr/CandidaDB

645

Candida

Genome

Candida albicans
genome database

http://www.candidagenome.org/

441

CYGD

MIPS
C
omprehensive
y
east
g
enome
d
atabase

http://mips.gsf.de/proj/yeast


483

Génolevures

A comparison of
S. cerevisiae

and
14 other yeast species

http://cbi.labri.fr/Genolevures

841

Mpact

Yeast protein
-
protein interaction data

http://mips.gsf.de/genre/proj/mpact

730

PROPHECY

Pro
filing of
phe
notypic
c
haracteristics in
y
east

http://prophecy.lundberg.gu.se/

576

SCMD

S
accharomyces
c
erevisiae

m
orphological
d
atabase: micrographs of
budding yeast mutants

http://yeast.gi.k.u
-
tokyo.ac.jp/

577

SCPD

S
accharomyces
c
erevisiae

p
romoter
d
atabase

http://rulai.cshl.edu/SCPD/

357

SGD

S
accharomyces

g
enome
d
atabase

http://www.yeastgenome.org/

25

TRIPLES

Tr
ansposon
-
i
nsertion
p
henotypes,
l
ocalization, and
e
xpression in
S
accharomyces

http://ygac.med.yale.edu/triples/

306

YDPM

Y
east
d
eletion
p
roject and
m
itoch
ondria database

http://www
-
deletion.stanford.edu/YDPM/YDPM_index.html

342

Yeast Intron Database

Ares lab database of splicesomal introns in
S. cerevisiae

http://www.cse.ucsc.edu/research/compbio/yeast_
introns.html

792

YEASTRACT

Yea
st
s
earch for
t
ranscriptional
r
egulators
a
nd
c
onsensus
t
racking

http://
www.yeastract.com

254

Yeast snoRNA
DB

Yeast
s
mall
n
ucle
o
lar RNAs

http://www.bio.umass.edu/biochem/rna
-
sequence/
Yeast_snoRNA_Database/snoRNA_DataBase.html

791

YGOB

Y
e
ast
g
ene
o
rder
b
rowser

http://wolfe.gen.tcd.ie/ygob

307

yMGV

Y
east
m
icroarray
g
lobal
v
iewer

http://www.transcriptome.ens.fr/ymgv/

531

YMPD

Yeast mitochond
rial protein database

http://bmerc
-
www.bu.edu/projects/mito/

763

YRC PDR

Yeast resource center public data repository

http://www.yeastrc.org/pdr/


5.7.2. Other fungi



425

CADRE

C
entral
A
spergillus

d
ata
re
pos
itory

http://www.cadre.man.ac.uk/

435

COGEME

Phytopathogenic fungi and oomycete EST database

http://cogeme.ex.ac.uk

815

FGDB

MIPS
Fusarium graminearum

g
enome
d
atabase

http://mips.gsf.de/genre/proj/fusarium/

525

Magnaporthe grisea

DB

Magnaporthe grisea

Database

http://www.broad.mi
t.edu/annotation/genome/magnap
orthe_grisea/Home.html

533

MNCDB

M
IPS

N
eurospora
c
rassa

d
ata
b
ase

http://mips.gsf.de/proj/neurospora/

708

OGD

Oomycete Genomics Database: ESTs and annotation

http://www.oomycete.net/

852

PHI
-
base

Genes affecting fungal pathogen
-
host interactions

http://www4.rothamsted.bbsrc.ac.uk/phibase/

98

Phytophthora

Functio
-
nal Genomics
DB

ESTs and expression data from
P. infestans

and
P. sojae

http://www.pfgd.org/pfgd/


5.8. Invertebrates




5.8.1.
Caenorhabditis elegans



430

C. elegans

Project

Genome sequencing data at the Sa
nger Institute

http://www.sanger.ac.uk/Projects/C_elegans

238

Intronerator

Intron
s and splicing in
C. elegans

and
C. briggsae

http://www.
cse.ucsc.edu/~kent/intronerator/

570

RNAiDB

RNAi phenotypic analysis of
C. elegans

genes

http://www.rnai.org/

864

SGCEdb

Structural genomics of
C. elegans

No longer maintained

304

WorfDB

C. elegans

ORFeome

http://worfdb.dfci.harvard.edu/

51

WormBase

Data repository for
C. elegans

and
C. briggsae
:

curated genome
annotation, genetic and physical maps, pathways

http://www.wormbase.
org/

961

WormBook

Peer
-
reviewed chapters on the biology of
C. elegans

http://www.wormbook.org


5.8.2.
Drosophila melanogaster



774

DPDB

D
rosophila

p
olymorphism
d
atabase

http:
//dpdb.uab.es/

928

DroID

Drosophila

gene and protein interaction data

http://www.droidb.org/

449

Drosophila

microarray
centre

Canadian
Drosophila

microarray centre

http://www.flyarrays.com/

924

DroSpeGe

Drosoph
ila

Species Genomes

http://insects.eugenes.org/DroSpeGe/

816

FLIGHT

Drosophila

phenotypes, gene expression and protein interaction
s

http://flight.licr.org/

71

Fl
yBase

Drosophila

sequences and genomic information

http://flybase.org/

767

FlyBrain

Database of the
Drosophila

nervous system

http://flybrain.neurobio.arizona.edu/

670

FlyMine

Integration of insect ge
nomic and proteomic data

http://www.flymine.org

817

FlyRNAi DRSC

Genome
-
wide RNAi analysis data in
Drosophila

http://flyRNAi.org/cgi
-
bin/RNAi_screens.pl

10
73

FLYSNP

S
ingle nucleotide polymorphism data for
Drosophila

melanogaster

http://flysnp.imp.univie.ac.at

1158

FlyTF

Drosophila

Transcription Factors

http://www.mrc
-
lmb.cam.ac.uk/genomes/FlyTF/

467

FlyTrap

Drosophila

mutants created using protein trap strategy

http://flytrap.med.yale.edu/

14

FlyView

Drosophila

development and genetics

http://flyview.uni
-
muenster.de/

471

GadFly

Genome annotation database of
Drosophila


http://www.fruitfly.org

677

GeniSys

Enhancer
-

and promoter
-
inserted mutants of
Drosophila

http://genisys.kaist.ac.kr:8080

989

GenomeRNAi

Cell
-
based RNAi phenotypes database

http://www.dkfz.de/signaling/ernai/ernai.html

8

Homophila

Drosophila

homologs of human disease genes

http://superfly.ucsd.edu/homophila/

509

InterActive Fly

Drosophila

genes and their roles in development

http://www.sdbonline.org/fly/aimain/1aahome.htm

1128

REDfly

Re
gulatory modules and transcription factor binding sites in
Drosophila

http://redfly.ccr.buffalo.edu


5.8.3. Other invertebrates



63

ACeDB

C. elegans
,
S. pombe
, and human genomic information

http://www.acedb.org/

11
52

AphidBase

Genomic database for the pea aphid (
Acyrthosiphon pisum
)

http://www.aphidbase.com/

410

AppaDB

Datab
ase on the nematode
Pristionchus pacificus

http://a
ppadb.eb.tuebingen.mpg.de

643

BeetleBase

Genome database of the beetle
Tribolium castaneum

http://www.bioinformatics.ksu.edu/BeetleBase/

1052

ButterflyBase

Genomics of butterflies (
Lepidopte
ra
)

http://www.butterflybase.org

649

Ciliate IES
-
MDS Db

Macro
-

and micronuclear genes in spirotrichous ciliates

http://oxytricha.princeton
.edu/dimorphism/database.ht
m

434

CnidBase

Cnidarian evolution and gene expression database

http://cnidbase.bu.edu/

653

CuticleDB

Structural proteins of Arthropod cuticle

http://bioinformatics.biol.uoa.gr/cuticleDB.

698

LumbriBASE

ESTs of the earthworm
Lumbricus rubellus


http://www.earthworms.org

543

Nematode.net

Parasitic nematode sequencing project

http://nematode.net/

544

NEMBASE

Nematode sequence and functional data database

http://www.nematodes.org

726

PPNEMA

P
lant
-
p
arasitic
nema
tode rRNAs

http://www.ppnema.uniba.it/

1006

Pris
tionchus.org

Genome data of the nematode <I>Pristionchus pacificus</I>

http://www.pristionchus.org

1161

Sebida

Sex bias in insect gene expression database

http://www.sebida.
de

743

SilkDB

Silk
worm

Bombyx mori

ESTs, mutants, photographs

http://www.ab.a.u
-
tokyo.ac.jp/genome/

744

SilkSatDb

A micro
sat
ellite database of the
silk
worm
Bombyx mori

http://210.212.212.7:9999/PHP/SILKSAT/index.php

1133

SmedGD

The
Schmidtea mediterranea

genome database

http://smedgd.neuro.utah.edu

747

SpodoBase

Genomics of the butterfly
Sp
odoptera frugiperda


http://bioweb.ensam.inra.fr/spodobase/

871

StellaBase

Nematostella vectensis

(sea anemone) genome

http://stellabase.org.

873

Tetrahymena

Genome
DB

Tetrahymena thermophila

genome database

http://www.ciliate.org

1031

VectorBase

Invertebrate Vectors of Human Pathogens

http://www.vectorbase.org

925

wFleaBase

Dap
hnia Water Flea Genome Database

http://wfleabase.org/


6. Metabolic Enzymes and Pathways; Signaling Pathways



898

Pathguide

A listing of pathway, signal transduction and protein
-
protein
interaction databases

http://pathguide.org


6.1. Enzymes and
e
nzyme
n
omenclature



421

BRENDA

Enzyme names and biochemical properties

http://www.brenda
-
enzymes.info/

109

ENZYME

Enzyme nomenclature and properties

http://www.expasy.org/enzyme/

459

Enzyme Nomenclature

IUBMB Nomenclature Committee recommendations

http://www.chem.qmul.ac.uk/iubmb/enzyme/

613

EzCatDB

Enzyme Catalytic Mechanism Da
tabase

http://mbs.cbrc.jp/EzCatDB/

716

FCP

Functional coverage of the proteome by structures

http://cgl.imim.es/fcp/

508

IntEnz

Integrated enzyme database and enzyme nomenclature

http://www.ebi.ac.uk/intenz

893

MACiE

Mechanism, annotation and classification in enzymes: enzyme
reaction mechanisms

http://www.ebi.ac.uk/thornton
-
srv/databases/MACiE/

998

ORENZA

ORphan ENZymes database

http://www.orenza.u
-
psud.fr/

727

PRECISE

Predicted and Consensus Interaction Sites in Enzymes

http://precise.bu.edu/precisedb/

1121

PROCOGNATE

Protein cognate ligands for the domains in enzyme structu
res

http://www.ebi.ac.uk/thornton
-
srv/databases/procognate/index.html

758

SCOPEC

Mapping of catalytic function to domain structure

http://www.sbinf.org/~richard/enzome/

772

TECRdb

Thermodynamics of enzyme
-
catalyzed reactions

http://xpdb.nist.gov/enzyme_thermodynamics


6.2. Metabolic
p
athways



419

BioCarta

Onli
ne maps of metabolic and signaling pathways

http://www.biocarta.com/genes/allPathways.asp

420

BioCyc

Pathway/genome databases for many bacteria

http://biocyc.o
rg/

423

Biodegradative Strain
Database

Microorganisms that can degrade aromatic and other organic
compounds

http://bsd.cme.msu.edu/

644

BioSilico

Integrated access to various metabolic databases

http://biosilico.kaist.ac.kr

991

HMDB

The Human Metabolome Database: Curated human metabolite and
metabolism data

http://www.hmdb.ca

112

KEGG Pathway

Metabolic and regulatory pathways in c
omplete genomes

http://www.genome.jp/kegg/pathway.html

835

Lipid MAPS

Lipid metabolites and pathways strategy

http://www.lipidmaps.org

114

MetaCyc

Meta
bolic

pathways and enzymes from various organisms

http://metacyc.org

115

PathDB

Biochemical pathways, compounds and metabolism

No longer maintained

612

Reactome

Datab
ase of metabolic and signaling pathways

http://www.reactome.org
/

953

SYSTOMONAS

SYSTems biology of pseudOMONAS

http://www.systomonas.de
/

117

UM
-
BBD

University of Minnesota biocatalysis and biodegradation database

http://umbbd.msi.umn.edu/


6.3. Protein
-
protein Interactions



633

3DID

3D
i
nteracting
d
omains: Domain
-
domain interactions in proteins
http://3did.embl.de
/

with known 3D structures

1042

3D
-
Interologs

Protein
-
protein interactions in various evolutionary lineages

http://gemdock.life.nctu.edu.tw/3D
-
Interologs

796

AffinDB

Affinity data for protein
-
ligand complexes

http://www.agklebe.de/affinity

405

aMAZE

A system for the annotation, management, and analysis of
biochemical and signalling pathway networks

http://www.scmbb.ulb.ac.be/amaze/

1046

AtPID

Arabidopsis thaliana

Protein Interactome Database

http://atpid.biosino.org/

1048

Bacteriome.org

Protein interaction database for E. coli

http://www.bacteriome
.org

103

BIND

B
iomolecular
i
nteraction
n
etwork
d
atabase

No longer free for all

1049

Binding MOAD

Binding Mother of All Databases: protein
-
ligand crystal structures

http://www.BindingMOAD.org

800

BioGRID

Genetic and physical interactions in yeast, worm
and fly

http://www.thebiogrid.org

422

BRITE

Biomolecular Relations in Information Transmission and
Expression

http://www.genome.ad.jp/brite

980

CellCircuits

Molecul
ar network models: from pairwise molecular interactions to
whole pathways

http://www.cellcircuits.org

1060

CORUM

Experimentally verified mammalian protein complexes

http://mips.gsf.de/genre/proj/corum

946

CutDB

Community annotation resource for proteases, their substrates
and cleavage sites

http://cutdb.burnham.org/

659

DDIB

Database of domain interactions and binding

http://www.ddib.org/

1066

DIMA

Domain interaction map: experimental data and predictions on
protein domain interactions

http://mips.gsf.de/genre/proj/dima2

104

DIP

Database of interacting proteins: Experimentally
-
determined
protein
-
protein interactions

http://dip.doe
-
mbi.ucla.edu

1155

Dockground

Protein
-
protein interfaces in co
-
crystallized protein structures

http://dockground.bioinformatics.ku.edu/

1067

DOMINE

Known and predicted protein domain interactions in PDB entries

http://domine.utdallas.edu

1033

DOMINO

Domain pe
ptide interactions

http://mint.bio.uniroma2.it/domino/

105

DRC

Database of ribosomal crosslinks

http://www.mpimg
-
berlin
-
dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc/

1086

HotSprint

Hot spots (functionally and structurally important residues) in
protein interfaces

http://prism.ccbb.ku.edu.tr/hotsprint/

664

hp
-
DPI

Database

of protein interactions in
Helicobacter pylori


http://dpi.nhri.org.tw/hp/

688

HPID

Human protein interaction database

http://www.hpid.org

897

I2D

Interologous Interaction Database: Predicted protein
-
protein
interac
tions in humans

http://ophid.utoronto.ca/i2d

507

IntAct

Protein
-
protein interaction data

http://www.ebi.ac.uk/intact/

770

Inter
-
Chain Beta
-
Sheets

Protein interacti
ons mediated by interchain beta
-
sheet formation

http://www.igb.uci.edu/servers/icbs/

510

InterDom

Putative protein domain interactions

http://interdom.
i2r.a
-
star.edu.sg/


138

KDBI

Kinetic data of bio
-
molecular interactions

http://bioinf.xmu.edu.cn/databases/kdbi/kdbi.php

1091

LigAsite

Biologically relevant binding sites in proteins with known structures

http://www.scmbb.ulb.ac.be/Users/benoit/LigASite

942

MiMI

Michigan Molecular Interactions:
P
rotein
-
protein interactions

http://mimi.ncibi.org/MiMI/home.jsp

1032

MINT

Molecular INTeraction

http://mint.bio.uniroma2.it/mint/

897

OPHID

O
n
line
p
redicted
h
uman
i
nteraction
d
atabase

Superseded by I2D (no. 897)

718

PDZBase

Protein
-
protein interactions involving PDZ domains

http://icb.med.cornell.edu/services/pdz/start

1111

PepCyber
:P~Pep

Human protein interactions mediated by phosphoprotein
-
binding
domains

http://PepCyber.umn.edu/PepCyber

773

PINdb

Proteins interacting in nucleus (human and yeast)

http://pin.mskcc.org

748

POINT

Prediction of human protein
-
protein interactome

http://point.bioinformatics.tw

729

ProNIT

Protein
-
nucleic acid interactions

http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.ht
ml

943

PROTCOM

3D structures of two
-
chain protein complexes

http://www.ces.clemson.edu/compbio/protcom

616

PSIbase

Interaction of proteins with known 3D structures

http://psimap.org/index.php/PSIMAP

1012

SNAPPI

Structures, iNterfaces and Alignments for Protein
-
Protein
Interactions

http://www.compbio.dundee.ac.uk/SNAPPI/download
s.jsp

1134

STITCH

Search Tool for Interactions of Chemicals

http://stitch.embl.de

749

Structurally conserved
interfaces

Interacting resi
dues

in protein
-
protein interfaces in PDB

http://home.ku.edu.tr/~okeskin/INTERFACE/INTERF
ACES.html

1138

The Cell Cycle DB

Genes and proteins involved in human and yeast cell cycle

http://www.itb.cnr.it/cellcycle

960

UniHI

Unified Human Interactome: human protein
-
protein interactions

http://www.mdc
-
berlin.de/unihi


6.4. Signaling
p
athways



419

BioCarta

Online maps of metabolic and signaling pathways

http://www.biocarta.com/genes/allPathways.asp

794

Cyclonet

Datab
ase on cell cycle regulation

http://cyclonet.biouml.org/index.html

890

EndoNet

Information on endocrine networks

http://endonet.bioinf.med.uni
-
goettingen.de/

1038

Hedgehog signalling

Resources and annotati
ons of the Hedgehog signaling pathway

http://hedgehog.sfsu.edu/

1104

NetworKIN

Network approach to human protein kinases and their substrate
s

http://networkin.info/

1112

Ph
osPhAt

Arabidopsis

Protein Phosphorylation Site Database

http://www.plantenergy.uwa.edu.au/applications/phos
phat/index.html

1175

PRRDB

Pattern recognition receptors and th
eir ligands

http://www.imtech.res.in/raghava/prrdb/

858

pSTIING

Protein signalling, transcriptional interactions and inflammation
networks gateway

http://pstii
ng.licr.org/

571

ROSPath

Reactive oxygen species (ROS) signaling pathway

http://rospath.ewha.ac.kr

395

STCDB

Signal Transduction Classification Database

http://bibiserv.techfak.uni
-
bielefeld.de/stcdb/

1142

UCSD
-
Nature Signaling
Gateway

Expert
-
authored and peer
-
reviewed information on mammalian
proteins involved in cellular signaling

http:/
/www.signaling
-
gateway.org/molecule/



7. Human and other Vertebrate Genomes




7.1. Model organisms, comparative genomics



879

ABA

Ascidian body atlas: digital 3D model of ascidian development

http://ciona.lab.nig.ac.jp/ascidian/top.html

974

AgBas
e

GO annotations for agriculturally important plants and animals

http://www.agbase.msstate.edu/

26

AllGenes

Human and mouse gene, transcript and protein annotation

http
://www.allgenes.org

957

Animal Genome Size
Database

Genome sizes of vertebrates and invertebrates

http://www.genomesize.com

975

AnimalQTLdb

Quantitative trait loci in livestock animals

http://www.animalgenome.org/QTLdb/

65

ArkDB

Genome databases for farm and other animals

http://www.thearkdb.org/

12

BodyMap

Human and mouse gene expression data

http://bodymap.ims.u
-
tokyo.ac.jp/

881

BodyMap
-
Xs

C
ross
-
species comparison of vertebrate gene expression

http://bodymap.jp/

647

ChickVD

Sequence variation in the chicken genome

http://chicken.genomics.org.cn

286

Cre Transgenic D
B

Cre transgenic mouse lines with links to publications

http://www.mshri.on.ca/nagy/

337

CORG

COmparative Regulatory Genomics:

co
nserved non
-
coding blocks


http://corg.molgen.mpg.de

808

DBTGR

Datab
ase of tunicate
Ciona

gene regulation

http://dbtgr.hgc.jp/

660

DED

Database of evolutionary distances

No l
onger maintained

20

Edinburgh Mouse Atlas

Digital atlas of mouse embryonic development

http://genex.hgu.mrc.ac.uk

453

EGO

Eukaryotic Gene Orthologs

http://compbio.dfci.harvard.edu/tgi/ego/

27

Ensembl

Annotated

information on eukaryotic genomes

http://www.ensembl.org/

396

euGenes

Genomic Information for Eukaryotic Organisms

http://eugenes.org/

1071

EuroPhenome

Large
-
scale phenotyping
of knockout mouse lines

http://www.europhenome.eu

673

GALA

Genomic alignment, annotation and experimental results

http://gala.cse.psu.edu/

1076

Gallus Gbrowse

Genomic inf
ormation on chicken and other avian species

http://birdbase.net/

1173

GEISHA

Gallus expression in situ hybridization analysis

http://geisha.arizona.edu

15

GXD

Mouse Gene Expression Database

http://www.informatics.jax.org/menus/expression_me
nu.shtml

605

HomoloGene

Automatically detected homologous genes in complete eukaryotic
genomes

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=ho
mologene

8

Homophila

Drosophila

homologs of human disease genes

http://superfly.ucsd.edu/homophila/

400

KOG

Eukaryotic Orthologous

Groups of proteins

http://www.ncbi.nlm.nih.gov/COG/

952

MamPol

Mammalia Polymorphism Database

http://mampol.uab.es

839

MFunGD

MIPS mouse functional genomics database

http://mips.gsf.de/genre/proj/mfungd

87

Mouse Genome
DB

Formerly mouse genome database

http://www.informatics.jax.org

995

Mouse Phenome
DB

phenotypic and

genotypic data from inbred strains of mice

http://www.jax.org/phenome

537

Mouse SAGE

SAGE libraries from various mouse tissues and cell lines

http://mouse.biomed.c
as.cz/sage

540

Mouse Transposon
Insertion Database

Mouse Transposon Insertion Database

http://mouse.ccgb.umn.edu/transposon/

152

Mouse Tumor Biology


Tumor types, genes, classification, incidence, p
athology

http://tumor.informatics.jax.org

598

Non
-
Human Genome
Segmental Duplication
D
B

Segmental duplications in mouse, dog and chicken genomes

http://proje
cts.tcag.ca/xenodup

548

OMIA

Online Mendelian Inheritance in Animals

http://omia.angis.org.au/

553

ParaDB

Paralogy mapping in human genomes

http://abi.marseille.inserm.fr/paradb/

554

PathBase

Europ
ean mutant mice histopathology database: images

http://www.pathbase.net/

1110

PBmice

piggyBac transposon insertions in the mouse genome.

http://www.scbit.org/PBmice/

55
6

PEDE

Pig Expression Data Explorer: Pig cDNA libraries and ESTs

http://pede.dna.affrc.go.jp

936

PigGIS

Pig genome mapping, genes and ESTs

http://pig.genomics.org.cn/

93

Rat Genome Database

Rat genetic and genomic data

http://rgd.mcw.edu

625

RatMap

Rat genome tools and data

http://ratmap.org

574

RTCGD

Retroviral Tagged Cancer Gene Database

http://rtcgd.ncifcrf.gov/

1164

SPEED

Searchable prototype experimental evolutionary database

http://bioinfobase.umkc.edu/speed/speed_main.htm

751

TAED

Th
e Adaptive Evolution Databas
e
:
plant and chordate gene families

http://www.bioinfo.no/tools/TAED

875

TreeFam

Tree families database: phylogenetic trees of animal genes

http://www.treefam.org

1144

UniTrap

Unambiguous insertions in the same subgenic regions of annotated
mouse genes

http://unitrap.cbm.fvg.it/

1145

UTGB/medaka

University of Tokyo Genome Browser of medaka fish (
O
ryzias
latipes
) genomic data

http://medaka.utgenome.org/

784

VEGA

Vertebrate genome annotation: a repository for manual annotation
of finished vertebrate genome sequences

http://vega.sanger.ac.uk/

1150

XenBase

Xenopus

genomics resource

http://www.xenbase.org

101

ZFIN

Zebrafish information network

http://zfin.org/


7.2. Human genome databases, maps and viewers



985

ENCODE Project

Encyclopedia of DNA Elements, all functional elemen
ts in the
human genome

http://genome.ucsc.edu/ENCODE

56

GDB

Human genes and genomic maps

http://www.gdb.org

35

Gene Resource Locator

Alignment of ESTs with finished human s
equence

No longer maintained

326

GeneAnnot

Revised annotation of Affymetrix human gene probe sets

http://genecards.weizmann.ac.il/geneannot/

350

GeneCards

Integrated database of human genes, map
s, proteins and diseases

http://bioinfo.weizmann.ac.il/genecards/

348

GeneLoc

Gene location database

http://genecards.weizmann.ac.il/geneloc/

59

GenMapDB

Mapped human BAC clones

http://genomics.med.upenn.edu/genmapdb

324

HOWDY

Human organized whole genome database

http://www
-
alis.toky
o.jst.go.jp/HOWDY/

77

Human BAC Ends D
B

Non
-
redundant human BAC end sequences

http://www.tigr.org/tdb/humgen/bac_end_search/bac_
end_intro.html

597

Human Genome Seg
-
mental D
uplication D
B

Segmental duplications in the human genome

http://projects.tcag.ca/humandup

61

IXDB

Physical maps of human chromosome X

http://ixdb.mpimg
-
berlin
-
dahlem.mpg.de

54

Map Viewer

Display of genomic information by chromosomal position

http://www.ncbi.nlm.nih.gov/mapview/

859

QTL Matchmaker

Quantitative trait loci mapping in human, mouse and r
at

http://pmrc.med.mssm.edu:9090/QTL/jsp/qtlhome.jsp

62

RHdb

Radiation hybrid map data

http://www.ebi.ac.uk/RHdb

592

SKY/M
-
FISH and CGH

Fluorescent images of chromosomes and cytogenetic data

http://www.ncbi.nlm.nih.gov/sky/

596

The Chromosome 7
Annotation Project

Human chromosome 7 sequence and annotation

http://www.chr7.org

684

TRBase

Tandem repeats in the human genome

http://trbase.ex.ac.uk/

316

UCSC Genome
Browser

Genome assemblies and annotation

http://genome.ucsc.edu/

319

UniSTS

Unified view of sequence tagged sites with mapping data

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=uni
sts

1149

X:MAP

Annotation and visualization of genome structure for Affymetrix
exon array analysis

http://xmap.picr.man.ac.uk


7.3. Human proteins



911

Consensus CDS

Collaborative effort to identify a core set of human protein
s

http://www.ncbi.nlm.nih.gov/projects/CCDS/

1072

Evola

Human genes and their vertebrate orthologs

http://jbirc.jbic.or.jp/hinv/evola/

465

FANTOM

Functional annotation of mouse full
-
length cDNA clones

http://fantom2.gsc.riken.go.jp

37

FLJ
-
DB

Annotated full
-
length human cDNAs

(formerly HUNT database)

http://fldb.hgc.jp/cgi
-
bin/cDNA3/public/publication/index.cgi

1037

GeneSpeed

Protein domains in the expressed human, mouse, fly and worm
genes

http://genespeed.ccf.org

685

H
-
InvDB

Full
-
length human cDNA clones

http://www.h
-
invitational.jp/

687

Hoppsigen

Human and mouse homologous processed pseudogenes

http://pbil.univ
-
lyon1.fr/databases/hoppsigen.html

500

HPRD

Human protein reference database: domain architecture, post
-
translational modifications, and disease association

http://www.hprd.org

171

HUGE

Human unidentified gene
-
encoded large (>50 kDa) protein and
cDNA sequences

http://www.kazusa.or.jp/huge/

696

IPI

International Protein Index

http://www.ebi.ac.uk/IPI

522

LIFEdb

Localization, interaction and functions of human proteins

http://www.dkfz.de/LIFEdb

600

Mammalian Gene
Collection

Full
-
length open reading frame clones for huma
n, mouse, and rat
genes

http://mgc.nci.nih.gov/

545

NetAffx

Public Affymetrix probesets and annotations

http://www.affymetrix.com/

550

ORFDB

Collection of ORFs that are so
ld by Invitrogen

http://orf.invitrogen.com/

1028

PlasmID

A repository for collection and distribution of plasmid clones

http://plasmid.hms.harvard.edu/

4

STACK

Se
quence tag alignment and consensus knowledgebase

http://www.sanbi.ac.za/Dbases.html

220

SYSTERS

Systematic re
-
searching and clustering of proteins

http://syst
ers.molgen.mpg.de/

312

trome, trEST, trGEN

Databases of predicted human protein sequences

ftp://ftp.isrec.isb
-
sib.ch/pub/databases/

6

UniGene

Unified clusters of ESTs and full
-
length mRNA sequenc
es

http://www.ncbi.nlm.nih.gov/UniGene/


8. Human Genes and Diseases




8.1. General
h
uman
g
enetics
d
atabases



661

DG
-
CST

Disease gene conserved sequence tags

http://143.225.208.11/cst3/

57

GenAtl
as

Human genes, markers and phenotypes

http://www.genatlas.org/

479

Genetics Home
Reference

A general guide on human hereditary diseases

http://ghr.nlm.nih.gov/

680

HAGR

Hu
man ageing genomic resources: Genes related to ageing in
humans and model organisms

http://genomics.senescence.info/

683

HCAD

Human chromosome aberration database: Chromosomal
breakpoints and affected gen
es

http://www.pdg.cnb.uam.es/UniPub/HCAD/

133

HGMD

Human gene mutation database

Requires user registration

1087

Human PAML Browser

Positive selection in human genes detected through genome
comparis
on

http://mendel.gene.cwru.edu/adamslab/pbrowser.py

1100

MSY Breakpoint
Mapper

Sequence
-
tagged sites in the human Y chromosome

http://break
pointmapper.wi.mit.edu

1102

MutDB

Predicted biochemical effects of human genetic variation: maping of
SNPs on protein sequence and structure

http://mutdb.org/

143

OMIM

Online Mendelian inheritance in man: A catalog of h
uman genetic
and genomic disorders

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OM
IM

1163

SNP2NMD

Human SNPs causing nonsense
-
mediated mRNA decay

http://variome.kobic.re.kr/SNP2NMD/


8.2. General polymorphism databases



119

ALFRED

Allele frequencies and DNA polymorphisms

http://alfred.med.yale.edu

793

CTGA

Datab
ase for genetic disorder
s in Arabs

http://www.cags.org.ae

654

Cypriot national
mutation database

Disease mutations in the Cypriot population

http://www.goldenhelix.org/cypriot/

125

Cytokine Gene Poly
-
morphism Database

Cytokine gene polymo
rphism literature database

http://www.nanea.dk/cytokinesnps/

655

Database of Genomic
Variants

Human genomic variants: frequency, segmental duplications and
genome assembly gaps

http://projects.tcag.ca/variation/

595

dbQSNP

Quantification of SNP allele frequencies database

http://qsnp.gen.kyushu
-
u.ac.jp/

886

dbRIP

Human retrotransposon insertion polymorphism

http://falcon.roswellpark.org:9090/

127

dbSNP

Database of single nucleotide polymorphisms

http://www.ncbi.nlm.nih.gov/SNP/

966

D
-
HaploDB

Definitive haplo
type database

http://orca.gen.kyushu
-
u.ac.jp

669

FESD

Functional Element SNPs Database: SNPs located within
promoters, UTRs, etc., of human genes

http://sysbio.kribb.re.kr/FESD/



1020

FINDBase

Frequencies of INherited Disorders

http://www.findbase.org

1074

F
-
SNP

Functional effects of various human SNPs

http://compbio.cs.queensu.ca/F
-
SNP/

344

HapMap Project

A haplotype map of the human genome with patterns of DNA
sequence variation

http://snp.cshl.org

131

HGVbase

Human genome variation database
: Curated human
polymorphisms

http://hgvbase.cgb.ki.se

496

HGVS Databases

A compilation of human mutation databases

http://www.hgvs.org/

517

JSNP

Japanese SNP database

http://snp.ims.u
-
tokyo.ac.jp/

665

PhenomicDB

Comparison of phenotypes of orthologous genes in human and
model organisms

http://www.phenomicdb.de

973

PolyDoms

Human coding S
NPs mapped onto protein domains

http://polydoms.cchmc.org

724

Polymorphix

Datab
ase of sequence polymorphisms

http://pbil.univ
-
lyon1.fr/polymorphix/qu
ery.php

146

Protein Mutant D
B

Compilation of protein mutant data

http://pmd.ddbj.nig.ac.jp/

1011

SNAP

An integrated SNP Annotation Platform

http://platform.humgen.au
.dk/

1030

SNP@Ethnos

Human SNPs and genes that contain human ethnic variation

http://bioportal.kobic.re.kr/SNPatETHNIC/

626

SNPeffect & PupaSuite

Phenotypic effects of human coding SNPs

http://snpeffect.vib.be/

590

TopoSNP

Topographic database of non
-
synonymous SNPs

http://gila.bioengr.uic.edu/snp/toposnp

755

TPMD

Taiwan polymorphic microsatellite ma
rker database

http://tpmd.nhri.org.tw


8.3. Cancer
g
ene
d
atabases



122

Atlas of Genetics and
Cytogenetics in Onco
-
logy and Haematology

Cancer related genes, chromosomal abnormalities in oncology and
haematology,
and cancer
-
prone diseases

http://atlasgeneticsoncology.org/

593

Cancer Chromosomes

Cytogenetic, clinical, and reference information on cancer
-
related
aberrations

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=ca
ncerchromosomes

951

CancerGenes

Gene selection resource for cancer genome projects

http://cbio.mskcc.org/cancergenes

1053

CanGEM

Gene copy number changes in cancer

http://www.cangem.org/

431

CGED

Cancer Gene Expression Database

http://lifesciencedb.jp/cged/

651

COSMIC

Catalogue Of Somatic Mutations In Cancer: Sequence data,
samples and publications

http://www.sanger.ac.uk/perl/CGP/cosmic

126

Database of Germline
p53 Mutations

Mutations in human tumor and cell line p53 gene

http://www.lf2.cuni.cz/proj
ects/germline_mut_p53.ht
m

889

EHCO

Encyclopedia of hepatocellular carcinoma genes online

http://ehco.iis.sinica.edu.tw

822

HPTAA

Human potential tumor
-
associated antigens

http://www.bioinfo.org.cn/hptaa/

134

Human p53, human
hprt, rodent lacI and
rodent lacZ databases

Mutations at the human p53 and hprt genes; rodent transgenic lacI
and lacZ mutations

http://www.ibiblio.org/dnam/mainpage.html

362

IARC TP53 Database

Human TP53 somatic and germline mutations

http://www
-
p53.iarc.fr/index.html

833

ITTACA

Integrated tumor

transcriptome array and clinical data analysis

http://bioinfo.curie.fr/ittaca

1096

MethyCancer

Links between DNA methylation levels and cancer

http://methyc
ancer.genomics.org.cn

1026

OncoDB.HCC

Oncogenomic database of hepatocellular carcinoma

http://oncodb.hcc.ibms.sinica.edu.tw

153

Oral Cancer Gene DB

Cellular and molecular data for genes involved in o
ral cancer

Incorporated into TGDBs, no. 155

1125

PubMeth

Links between DNA methylation levels and cancer

http://matrix.ugent.be/pubmeth/

579

SNP500Cancer

Re
-
sequenced SNPs from 102 reference samples

http://snp500cancer.nci.nih.gov

149

SV40 Large T
-
Antigen
Mutant Database

Mutations in SV40 large tumor antigen gene

http://supernova.bio.pitt.edu/pipaslab/

922

Tumor Associated
Gene D
atabase

Tumor
-
associated genes database

http://www.binfo.ncku.edu.tw/TAG/GeneDoc.php

155

Tumor Gene Family
Databases (TGDBs)

Cellular, molecular and biological data about genes involved in
various cancers

http://www.tumor
-
gene.org/tgdf.html

768

ALPSbase

Autoimmune lymphoproliferative syndrome database

http://research.nhgri.nih.gov/ALPS/


8.4. Gene
-
, system
-

or disease
-
specif
ic

databases



788

AlzGene

Candidate genes for Alzheimer disease

http://www.alzgene.org

120

Androgen Receptor
Gene Mutations D
B

Mutations in the androgen receptor gene

http://www.mcgill.ca/androgendb/

393

AngioDB

Database of angiogenesis and angiogenesis
-
related molecules

http://angiodb.snu.ac.kr/

416

BayGenomics

Publicly available mouse gene trap cell lines

Superseded by

Gene Trap database, no. 827

417

BGED

Brain Gene Expression Database

http://genome.mc.pref.osaka.jp/BGED/

123

BTKbase

Mutation registry for X
-
linked agammaglobulinemia

http://bioinf.uta.fi/BTKbase/

594

CarpeDB

Comprehensive database on the genetics of epilepsy

http://www.carpedb.ua.edu

124

CASRDB

Calcium
-
sensing receptor database: CASR mutations causing
hypercalc
emia and/or hyperparathyroidism

http://www.casrdb.mcgill.ca/

137

Collagen Mutation D
B

Human type I and type III collagen gene mutations

http://www.le.ac.uk
/genetics/collagen/

887

DENIZ

Beta
-
thalassemia allele frequencies in world populations

No longer maintained

454

EICO DB

Expression
-
based Imprint Candidate Organiser

http://fantom2.gsc.riken.jp/EICODB/

110

EpoDB

Genes expressed during human
E
rythro
po
iesis

database

http://www.cbil.upenn.edu/EpoDB/

460

ERGDB

Estrogen Responsive Genes Database

http://sdmc.lit.org.sg/ergdb/cgi
-
bin/explore.pl

464

EyeSite

Families of proteins functioning in the eye

http://eyesite.cryst.bbk.ac.uk/

363

GOLD.db

Genomics Of Lipid
-
associated Disorders

http://gold.tugraz.at

130

HaemB

Factor IX gene mutations, insertions and deletions

http://www.kcl.ac.uk/ip/petergreen/haemBdatabase.
html

491

HbVar

Human hemoglo
bin variants and thalassemias

http://globin.cse.psu.edu/globin/hbvar

907

HDBase

A website for Huntington's disease research

http://hdbase.org/

493

HemBase

Genes exp
ressed in differentiating human erythroid cells

http://hembase.niddk.nih.gov/

494

HemoPDB

Hematopoietic Promoter Database

http://bioinformatics
.med.ohio
-
state.edu/HemoPDB

366

HORDE

Human Olfactory Receptor Data Exploratorium

http://bioinfo.weizmann.ac.il/HORDE/

293

HOX
-
PRO

Homeobox genes database

http://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/ho
x
-
pro00.html

499

HPMR

Human plasma membrane receptome: sequences, literature, and
expression data

http://receptome.stanfor
d.edu/

135

Human PAX2 Allelic
Variant Database

Mutations in human PAX2 gene

http://pax2.hgu.mrc.ac.uk/

136

Human PAX6 Allelic
Variant Database

Mutations in human PAX6 gene

http://pax6.hgu.mrc.ac.uk/

501

IL2Rgbase

X
-
linked severe combined immunodeficiency mutation database

http://research.nhgri.nih.gov/scid/

294

Imprinted Gene
Catalogue

Imprinted genes and parent
-
of
-
o
rigin effects in animals

http://igc.otago.ac.nz/home.html

506

INFEVERS

Hereditary inflammatory disorder and familial mediterranean fever
mutation data

http://f
mf.igh.cnrs.fr/infevers

949

KBERG

KnowledgeBase for Estrogen Responsive Genes

http://research.i2r.a
-
star.edu.sg/kberg

139

KinMutBase

Disease
-
causing protein kinase mutations

http://www.uta.fi/imt/bioinfo/KinMutBase/

523

Lowe Syndrome
Mutation Database

Mutations causing Lowe oculocerebrorenal syndrome

http://research.nhgri.nih.gov/lowe/

142

NCL Resource

Polymorphisms in neuronal ceroid lipofuscinoses genes

http://www.ucl.ac.uk/ncl/

1025

NEIbank

EyeSAGE, EyeBrowse and Eye Disease Gene databases

http://neiban
k.nei.nih.gov

144

PAHdb

Mutations at the phenylalanine hydroxylase locus

http://www.pahdb.mcgill.ca

559

PGDB

Prostate and prostatic diseases gene database

http://www.uc
sf.edu/pgdb/

145

PHEXdb

PHEX mutations causing X
-
linked hypophosphatemia

http://www.phexdb.mcgill.ca

154

Prostate Expression D
B

Prostate expression database: ESTs from prostate tissue and cell
type
-
specific c
DNA libraries

http://www.pedb.org/

147

PTCH1 Mutation D
B

Mutations and SNPs found in PTCH1 gene

http://www.cybergene.se/cgi
-
bin/w3
-
msql/ptchbas
e/index.html

148

RB1 Gene Mutation D
B

Mutations in the human retinoblastoma (RB1) gene

http://www.verandi.de/joomla/

769

SCAdb

Spinocerebellar ataxia candidate gene database

http://ymbc.ym.edu.tw/sca_ensembl/

787

SynDB

Synapse protein database

http://syndb.cbi.pku.edu.cn

632

T1Dbase

A resource for type 1 diabetes research

http:/
/t1dbase.org

752

The Autism Chromo
so
-
me Rearrangement D
B

Curated collection of genomic features related to autism

http://projects.tcag.ca/autism

753

The Lafora Database

The Lafora
progressive myoclonus epil
epsy mutation and
polymorphism dat
abase

http://projects.tcag.ca/lafora/

907

T
-
REGs

A list of
T
GFbeta
-
re
sponsive
g
enes

No longer maintained


9. Microarray Data and other Gene Expression Databases



1043

4DX
press

Database for cross species expression pattern comparisons

http://ani.embl.de/4DXpress

634

5'SAGE

5'
-
end serial analysis of gene expression

http://5sage.gi.k.u
-
tokyo.ac.jp/

338

ArrayExpress

Public collecti
on of microarray gene expression data

http://www.ebi.ac.uk/arrayexpress

11

Axeldb

Gene expression in
Xenopus laevis

http://www.dkfz.de/en/mol
_embryology/axeldb.html

802

CAGE

CAGE tags for cap
-
analysis of gene expression

http://fantom31p.gsc.riken.jp/cage/mm5/

427

CATMA

Complete
Arabidopsis

Transcriptome MicroArray

http://www.catma.org

432

CleanEx

Expression reference database, linking heterogeneous expression
http://www.cleanex.isb
-
sib.ch/

data to facilitate cross
-
dataset comparisons

1064

CycleBase

G
ene expression profiles from cell
-
cycle microarray studies

http://www.cyclebase.org

657

dbERGEII

Database of experimental results on gene expression: Genomic
alignment, annotation and experimental data

http://dberge.cse.psu.edu/menu.html

1170

dbLEP

Database of Liver proteome expression profiles

http://lep.hupo.org.cn/main.htm

812

EMAGE

Edinburgh mouse atlas gene e
xpression database

http://genex.hgu.mrc.ac.uk/Emage/database

13

EPConDB

Gene expression in pancreatic development, beta cell function and
diabetes

h
ttp://www.cbil.upenn.edu/EPConDB

987

Gene Aging Nexus

Aging
-
related gene expression data

http://gan.usc.edu

24

Gene Expression in
Tooth Database

Gene expression in dental tissue

http://bite
-
it.helsinki.fi/

325

GeneNote

Human genes expression profiles in healthy tissues

http://genecards.weizmann.ac.il/genenote/

330

GenePaint

Gene expression patterns in the mouse

http://www.genepaint.org/Frameset.html

676

GeneTide

A transcriptome
-
focused member of the GeneCards suite

http://genecards.weizmann.ac.il/genetide/

481

GeneTrap

Expression patterns in an embryonic stem library of gene trap
insertions

http://www.cmhd.ca/genetrap/

918

GENSAT

Gene
E
xpression
N
ervous
S
ystem
A
tlas: a map of gene expression
in the central ner
vous system of the mouse

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=ge
nsat

603

GEO

Gene Expression Omnibus:
Public gene expression repository

http://www.ncbi.nlm.nih.gov/geo/

485

GermOnline

Gene expr
ession in mitotic and meiotic cell cycle

http://www.germonline.org/

891

GPX
-
Macrophage

Gene expression in macrophages

http://ebola.gti.ed.ac.uk
:8090/GPX/htdocs/index.html

23

HuGEIndex

Human Gene Expression Index: Expression levels in normal
tissues

http://zlab.bu.edu/HugeSearch

16

Interferon Stimulated
Gene Database

Genes induced by treatment with

interferons

http://www.lerner.ccf.org/labs/williams/xchip
-
html.cgi

827

International Gene Trap
Consortium

DB

Publicly available gene trap cell lines in mouse

http://www.genetrap.org/

17

Kidney Development
Database

Kidney development and gene expression

http://golgi.ana.ed.ac.uk/kidhome.html

778

LOLA

List of lists annotated: a comparison of

gene sets identified in
different microarray experiments

http://www.lola.gwu.edu/

1092

M3D

Many Microbe Microarrays Database

http://m3d.bu.edu/

18

MAGEST

Ascidian (Halocynthia roretzi) gene expression patterns

http://magest.hgc.jp/

699

MAMEP

Molecular Anatomy of the Mouse Embryo Project

http://mamep.molgen.mpg.de/

339

MEPD

Gene expression in medaka (freshwater fish Oryzias latipes)

http://www.embl.de/mepd/

541

NASCarrays

Nottingham
Arabidopsis

Stock Centre microarray database

http://affymetrix.arabidopsis.info

709

OncoMine

Cancer microarray dat
a by gene or cancer type

http://www.oncomine.org/

558

PEPR

Public Expression Profiling Resource

http://pepr.cnmcresearch.org

568

RefExA

Reference database for human
gene expression analysis

http://www.lsbm.org/site_e/database/index.html

739

rOGED

Rat ovarian gene expression database

http://app.mc.u
ky.edu/kolab/rogedendo.aspx

712

SAGEmap

NCBI's resource for SAGE data from various organisms

http://www.ncbi.nlm.nih.gov/SAGE

742

SIEGE

Smoking Induced Epithelial Gene Expression

http://pulm.bumc.bu.edu/s
iegeDB

22

Stanford Microarray DB

Raw and normalized data from microarray experiments

http://genome
-
www.stanford.edu/microarray

1139

TMAD

The Stanford Tissue Microarray Database

http://tma.stanford.edu

905

TmaDB

Tissue microarray database

http://www.bioinformatics.leeds.ac.uk/tmadb/






10. Proteomics Resources



606

2D
-
PAGE

Proteome database s
ystem for microbial research

http://www.mpiib
-
berlin.mpg.de/2D
-
PAGE

1050

Biodefense Proteomics
Resource Center

Proteomics and host
-
pathogen interactions for biodefense
-
related
microorganisms

http://www.proteomicsresource.org/default.aspx

731

DynaProt 2D

Proteome database of
Lactococcus lactis

http://www.wzw.tum.de/proteomik/lactis/

2
22

GELBANK

2D gel electrophoresis patterns of proteins from complete microbial
genomes

http://gelbank.anl.gov

950

MAPU

Max
-
Planck Unified proteome database

http://www.mapu
proteome.com

710

Open Proteomics DB

Mass
-
spectrometry
-
based proteomics data for human, yeast,
E. coli

and
Mycobacterium

http://bioinformatics.icmb.utexas.edu/OPD/

850

PepSeeker

Peptide identific
ation and ion information from proteome
experiments

http://nwsr.bms.umist.ac.uk/cgi
-
bin/pepseeker/pepseek.pl

851

PeptideAtlas

Peptides identified in LC
-
MS/MS proteomics experiments

http://www.peptideatlas.org

721

PlantMarkers

Datab
ase of predicted molecular markers from plants

http://markers.btk.fi


857

PRIDE

Proteomics peptide identification database

http://www.ebi.ac.uk/pride/

225

SWISS
-
2DPAGE

Annotated 2D gel electrophoresis database

http://www.expasy.org/ch2d/


11. Other Molecular Biology Databases



256

BioImage

Database of multidimensional biological images

http://www.bioimage.org/

801

BioModels

Published mathematical models of biological interest

http://www.ebi.ac.uk/biomodels/

1171

Déjà vu

Duplicate citations in the scientific literatu
re

http://spore.swmed.edu/dejavu/

298

PubMed

Citations and abstracts of biomedical literature

http://pubmed.gov

992

University of Pittsburgh
Bioinformatics
Resources Collec
tion

A collection of bioinformatic databases and software tools

http://www.hsls.pitt.edu/guides/genetics/obrc/

701

MetaRouter

Compounds and pathways related to bioremediation

http://pdg.cnb.uam.es/MetaRouter


11.1. Drugs and drug design



407

ANTIMIC

Database of natural antimicrobial peptides

http://research.i2r.a
-
star.edu.sg
/Templar/DB/ANTIMIC/

408

APD

Antimicrobial Peptide Database

http://aps.unmc.edu/AP/main.php

1055

CEBS

Database of toxicogenomics, microarray and proteomics data.

http://cebs.niehs.nih.gov

443

DART

Drug Adverse Reaction Targets

http://xin.cz3.nus.edu.sg/group/drt/dart.asp

811

DrugBank

Combined information on drugs and drug targets

http://redpoll.pharmacy.ualberta.ca/drugbank/

819

GLIDA

G
-
protein coupled receptors ligand database

http://pharminfo.pharm.kyoto
-
u.ac.jp/services/
glida/

1002

PharmGED

PharmacoGenetic Effect Database

http://bidd.cz3.nus.edu.sg/phg/

392

PharmGKB

Pharmacogenomics and Pharmacogenetics Knowledge Base

http://www.pha
rmgkb.org

741

Scorpion

Database of scorpion toxins

http://sdmc.i2r.a
-
star.edu.sg/scorpion/

902

SuperDrug

2D and 3D chemical structures of various drugs

http://bioinformatics.charite.de/superdrug

903

SuperNatural

Natural compounds and their suppliers

http://bioinformatics.charite.de/supernatural

1136

SuperTarget

Drug
-
related information: medical indications, adverse drug effects,
drug metabolism and Gene Ontology terms of the target proteins

http://insilico.charite.de/supertarget

315

TTD

Therapeutic target database

http://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp

1147

VIOLIN

Vacci
ne Investigation and Online Information Network

http://www.violinet.org


11.2. Molecular probes and primers



781

AOBase

Antisense oligonucleotide selection and design

http://www.bioit.org.cn/ao/aobase

505

IMGT/PRIMER
-
DB

Immunogenetics oligonucleotide primer database

http://imgt3d.igh.cnrs.fr/PrimerDB/Query_PrDB.pl

296

MPDB

Molecular Probe Database

http://www.biotech.ist.unige.it/interlab/mpdb.html

728

Primer Studio

PCR primers for eukaryotic and prokaryotic genes

http://bioinfo.ebc
.ee/PrimerStudio/

390

probeBase

rRNA
-
targeted oligonucleotide probe sequences, DNA microarray
layouts, and associated information

http://www.microbial
-
ecology.net/probebase

736

QPPD

Quantitative

PCR Primer Database

http://web.ncifcrf.gov/rtp/GEL/primerdb/default.asp

1008

qPrimerDepot

Quantitative real time PCR primers for human RefSeq sequences

http://primerdepot.nci.nih.gov/

356

RTPrimerDB

Real
-
time PCR primer and probe sequences

http://medgen.ugent.be/rtprimerdb/

303

VirOligo

Virus
-
specific oligonucleotides for PCR and hybridiz
ation

http://viroligo.okstate.edu


12. Organelle Databases



804

Chloroplast
g
enome D
B

Chloroplast genome database

http://chloroplast.cbio.psu.edu/

74

GOBASE

Organelle genome database

http://megasun.bch.umontreal.ca/gobase/gobase.ht
ml

713

Organelle DB

Organelle proteins and subcellular structures

http://organelledb.lsi.umich.edu/

601

Organelle genomes

NCBI's organelle genome resource

http://www.ncbi.nlm.nih.gov/genomes/ORGANELLE
S/organelles.html

1001

PeroxisomeDB

Per
oxisomal proteins, metabolic routes and diagnostic tools

http://www.peroxisomeDB.org

1115

Plant Organelles DB

Images and protocols for plant organelle research

http://podb.nibb.ac.jp/Organellome

722

PLprot

Plastid protein database

http://www.plprot.ethz.ch/


12.1. Mitochondrial Genes and Proteins



637

AMPDB

Arabidopsis

Mitochondrial Protein Database

http://www.plantenergy.uwa.edu.au/applications/am
pdb/index.html

686

HMPD

Human mitochondrial protein database

http://bioinfo.nist.gov/hmpd/

117
4

HmtDB

Human mitochondrial database

http://www.hmtdb.uniba.it/

824

Human MtDB

Human mitochondrial genome database

http://www.genpat.uu.se/mtDB

38

HvrBase++

Primate m
itochondrial DNA control region sequences

http://www.hvrbase.org

894

MamMiBase

Mammalian mitochondrial genome database

http://xavante.fmrp.usp.br/mammibase/

64

Mitochondriome

Metazoan mitochondrial genes

http://www.ba.itb.cnr.it/mitochondriome/

83

MitoDat

Mitochondrial proteins (predominantly human)

http
://www
-
lecb.ncifcrf.gov/mitoDat/

84

MITOMAP

Human mitochondrial genome

http://www.mitomap.org/

1099

Mitome

Comparative analysis of metazoan mitochondrial genomes

http://www.m
itome.info

86

MITOP2

Mitochondrial proteins, genes and diseases

http://www.mitop2.de/

532

MitoProteome

Experimentally described human mitochondrial proteins

http://www.m
itoproteome.org

538

MPIMP db

Mitochondrial protein import machinery of plants and yeast

http://www.plantenergy.uwa.edu.au/applications/mpi
mp/

547

OGRe

Organellar Genome Resource

http://ogre.mcmaster.ca


13. Plant Databases




13.1.
General plant databases




599

BarleyBase

Expression profiling of plant genomes

http://www.barleybase.org/

982

Cere
al Small RNA DB

Small RNAs expressed in rice and maize

http://sundarlab.ucdavis.edu/smrnas/

624

CR
-
EST

Cropp ESTs:
Barley, wheat, pea, and potato ESTs

http://pgrc.ipk
-
gatersleben.de/cr
-
est/

888

DRASTIC

Database resource for analysis of signal transduction in plant cells

http://www.drastic.org.uk

128

FLAGdb++

Integrative database about plant genomes

http://urgv.evry.inra.fr/projects/FLAGdb++/HTML/ind
ex.shtml

672

GabiPD

Central database of the German Plant Genome Project

http://gabi.rzpd.de

675

G
eneFarm

Expert annotation of
Arabidopsis

gene and protein families

http://urgi.versailles.inra.fr/Genefarm/

351

GénoPlante
-
Info

Plant genomic data from the Génoplante consortium

http://www.genoplante.com/

488

GrainGenes

Genes and phenotypes of wheat, barley, rye, triticale, oats

http://wheat.pw.usda.gov

607

Gramene

A resource for comparative grass genomics

http://www.gramene.org

1095

MetaCrop

Biochemical pathways and enzymes in crop plants

http://metacrop.ipk
-
gatersleben.de

1029

MIPSPlantsDB

MIPS Plants Databases

http://mips.gsf.de/proj/plant/jsf/

581

openSputnik

Plant EST clustering and functional annotation

No longer maintained

999

PathoPlant

Signal transduction related to plant
-
pathogen interactions

http://www.pathoplant.de

853

Phytome

Comparative genomics of plant species

http://www.phytome.org

956

Plant DNA C
-
values
Database

Genome sizes of various plants and algae

http://www.kew.org/genomesize/homepage.html

562

Plant Genome Central

NCBI’s portal for various large
-
scale plant genome and EST
sequencing projects

http://www.ncbi.nlm.nih.gov/genomes/PLANTS/Plant
List.html

843

Plant MPSS

Massively parallel signature sequencing of plant genes

http://mpss.udel.edu

1116

Plant Stress
-
Respon
si
-

Stress
-
responsiv
e gene in various plant species

http://dayhoff.generationcp.org

ve Gene Catalog

355

PlantGDB

Plant genome database: Actively
-
transcribed plant genes

http://www.plantgdb.org/

1118

PlantTribes

Families of protein
-
coding genes from five sequenced plant species

http://www.floralgenome.org/tribe.php

948

POGs/PlantRBP

Orthologous groups of RNA binding proteins in plants

http://plantrbp.uoregon.edu

1119

PPDB

Plant promoter database

http://ppdb.gene.nagoya
-
u.ac.jp

578

SeedGenes

Genes essential for
Arabidopsis

development

http://www.seedgenes.org/

940

TIGR Plant Transcript
Assembly database

Transcript assemblies of plant EST and cDNA sequences

http://plantta.tigr.org

313

TropGENE DB

Genes and genomes of sugarca
ne, banana, cocoa

http://tropgenedb.cirad.fr/

67

UK CropNet

Genome mapping in crop plants

http://ukcrop.net/


13.2.
Arabidopsis thaliana



636

AGNS

Arabidopsis

GeneNet supp
lementary

http://wwwmgs.bionet.nsc.ru/agns/

618

AGRIS

Arabidopsis

gene regulatory information server

http://arabidopsis.med.ohio
-
state.edu

780

Arabidopsis

MPSS

Arabidopsis

gene expression detected by

massively parallel
signature sequencing

http://mpss.udel.edu/at/

638

Arabidopsis

Nucleolar
Protein Database

Comparative analysis of human and
Arabidopsis

nucleolar
proteomes

http://bioinf.scri.sari.ac.uk/cgi
-
bin/atnopdb/proteome_comparison

640

Arabidopsis

Small RNA
Project

Arabidopsis

Small RNA sequences

http://asrp.cgrb.oregonstate.edu/

880

ARTADEdb

Arabidopsis

tiling
-
array
-
based detection of exons

http://omicspace.riken.jp/ARTADE/

394

AtGDB

Arabidopsis thaliana

genome database

http://www.plantgdb.org/AtGDB

765

AthaMap

Genome
-
wide map of putative transcription factor binding s
ites in
Arabidopsis thaliana

http://www.athamap.de/

934

ATTED
-
II

Coexpressed gene sets and gene regulators in
Arabidopsis

http://www.atted.bio.titech.ac.jp/

610

Bra
ssica BASC

Datab
ase for
Brassica

genomic research

http://hornbill.cspp.latrobe.edu.au/cgi
-
binpub/brassica/index.pl

1054

CATdb

Arabidopsis

transcriptome data

http://urgv.evry.inra.fr/CATdb

656

DATF

Database of
Arabidopsis

transcription factors

http://datf.cbi.pku.edu.cn

935

GABI
-
Kat

Flanking sequence tags for T
-
DNA insertions in
Arabido
psis

http://www.GABI
-
Kat.de

1081

GreenPhylDB

Comparative genomics of rice and
Arabidopsis

thaliana

http://greenphyl.cirad.fr

527

MAtDB

MIPS
Arabidopsis thaliana

database

http://mips.gsf.de/proj/thal/db

1004

PlantQTL
-
GE

Quantitative trait locus analysis in
Arabidopsis

and rice

http://www.scbit.org/qtl2gene

738

RARGE

RIKEN
Arabidop
sis

genome encyclopedia: cDNAs, mutants and
microarray data

http://rarge.gsc.riken.jp/

97

TAIR

The
Arabidopsis

information resource

http://www.arabidopsis.org/

627

WAtDB

Wageningen
Arabidopsis thaliana

Database

No longer maintained


13.3.
Rice



418

BGI
-
RISe

Beijing Genomics Institute Rice Information System

http://rise.genomics.org.cn/

1156

DRTF

Database of Rice Transcription Factors

http://drtf.cbi.pku.edu.cn/

79

INE

Integrated rice genome explorer

http://rgp.dna.affrc.go.jp/giot/INE.html

353

IRIS
-

International Rice Information System

http://www.iris.irri.org

536

MOsDB

MIPS Oryza sativa database

http://mips.gsf.de/proj/plant/jsf/rice/index.jsp

848

OryGenesDB

Rice genes, T
-
DNA and Ds flanking sequence tag
s

http://orygenesdb.cirad.fr/

628

Oryza Tag Line

T
-
DNA insertion mutants of rice

http://urgi.versailles.inra.fr/OryzaTagLine/

90

Oryzabase

Rice gene
tics and genomics

http://www.shigen.nig.ac.jp/rice/oryzabase/

860

RAP
-
DB

Rice annotation project database

http://rapdb.dna.affrc.go.jp/

737

Rice Anno
tation DB

Contig data for manual annotation of rice genome

http://golgi.gs.dna.affrc.go.jp/SY
-
1102/rad/index.html

861

Rice Mutant Database

Rice mutant database

http://rmd.ncpgr.cn/

56
9

Rice Pipeline

Unification tool for rice databases

http://cdna01.dna.affrc.go.jp/PIPE

572

Rice Proteome DB

Rice proteome database

http://gene
64.dna.affrc.go.jp/RPD/main_en.html

336

RiceGAAS

Rice genome automated annotation system

http://ricegaas.dna.affrc.go.jp/


13.4.
Other plants



971

ForestTreeDB

Annotated ESTs from diverse organs of con
ifer and poplar trees

http://foresttree.org/ftdb

1078

Genome Database for
Rosaceae

Genetics and genomics data on apple, cherry, peach, pear,
raspberry, rose and strawberry

http://www.bioinfo.wsu.edu/gdr/

80

Legume Information
System

Legume information server (formerly Medicago genome initiative):
ESTs, gene expression and proteomic data

http://www.comparative
-
legume
s.org/

526

MaizeGDB

Maize genetics and genomics database

http://www.maizegdb.org

1159

MedicCyc

Biochemical pathways in Medicago truncatula

http://www.noble.org/medicc
yc/

539

MtDB

<I>Medicago trunculata</I> Database

http://www.medicago.org/MtDB

921

NRESTdb

Natural Rubber EST Database

http://genome.ukm.my/nrestdb/

849

Panzea

Maize genome project data

http://www.panzea.org

620

PoMaMo

Potato Maps and More

https://gabi.rzpd.de/PoMaMo.html

766

SGMD

Soybean genomics and microarray database

http://psi081.ba.ars.usda.gov/SGMD/d
efault.htm

1132

Shanghai Rapeseed
Database

Seed development and fatty acid metabolism of oilseed crops

http://rapeseed.plantsignal.cn

919

SoyBase

Genetic, genomic and phenotypic information about soybean

http://soybase.org

870

SoyGD

Soybean genome database

http://soybeangenome.siu.edu

872

TED

Tomato expression database

http://ted.bt
i.cornell.edu

874

TIGR Maize database

Maize genome sequencing consortium site

http://maize.tigr.org

1016

TomatEST DB

EST collection from multiple tomato species

http://bio
srv.cab.unina.it



14. Immunological Databases



799

AntiJen

Quantitative binding data for peptides and proteins of
immunological interest

http://www.jenner.ac.uk/AntiJen

642

BCIpep

Datab
ase of B
-
cell e
pitopes

http://bioinformatics.uams.edu/mirror/bcipep/

604

dbMHC

Genetic and clinical database of the human MHC

http://www.ncbi.nlm.nih.gov/mhc/

813

Epitome

Antigenic epitopes in proteins and antibodies that bind them

http://predictprotein.org/AifoEpi/

150

FIMM

Functional molecular immunology data

http://research.i2r.a
-
star.edu.sg/fimm

682

Haptendb

Curated database of hapten molecules

http://www.imtech.res.in/raghava/haptendb/

172

IMGT

International immunogenetics information system
:
Immunoglobulins, T cell receptors, MHC, and RPI

http://imgt.cines.fr

503

IMGT/GENE
-
DB

Vertebrate immunoglobulin and T cell receptor genes

http://imgt.cines.fr
/cgi
-
bin/GENElect.jv

173

IMGT/HLA

Polymorphism of human MHC and related genes

http://www.ebi.ac.uk/imgt/hla/

504

IMGT/LIGM
-
DB

Immunoglobulin, T cell receptor and MHC nucleotide sequences
from human and othe
r vertebrates

http://imgt.cines.fr/cgi
-
bin/IMGTlect.jv

779

Immune epitope
DB

Antibody and T cell epitopes for primates, rodents, and other
animals

http:/
/www.immuneepitope.org/

367

IPD

Immuno Polymorphism Database

http://www.ebi.ac.uk/ipd/

692

IPD
-
ESTDAB

Immunologically characterised melanoma cell lines

http://www.ebi.ac.uk/ipd/

693

IPD
-
HPA

Human platelet antig
ens

http://www.ebi.ac.uk/ipd/

694

IPD
-
KIR

Killer
-
cell Immunoglobulin
-
like Receptors

http://www.ebi.ac.uk/ipd/

691

IPD
-
MHC

Sequences of the major histocompatibility complex

http://www.ebi.ac.uk/ipd/mhc

361

Je
nPep

Quantitative binding data for peptides and proteins of
immunological interest

Superseded by AntiJen, no. 799

702

MHCBN

Datab
ase of MHC binding and non
-
binding peptides

http://www.imtech.res.in/ra
ghava/mhcbn/

181

MHCPEP

MHC
-
binding peptides

http://bio.dfci.harvard.edu/DFRMLI/

1101

MUGEN Mouse D
B

Murine models of immune processes and immunological diseases

h
ttp://www.mugen
-
noe.org/database/

967

SuperHapten

A comprehensive database for small immunogenic compounds

http://bioinformatics.charite.de/superhapten

621

VBASE2

Variable genes from the Ig lo
ci of human and mouse

http://www.vbase2.org/



a



Each database is shown in the list only once. In another version of this list, available at the NAR web site
http://www.oxfordjournals.org/na
r/database/a/
, a
database can be listed under two (sub)categories.

b



Accession number of the database in the on
-
line list; can be used to view the database summary. For example,
http:
//www.oxfordjournals.org/nar/database/summary/1

shows the summary for DDBJ.

c



In some database names, the word "database" is abbreviated as

DB

.