Databases in bioinformatics - ICGEB

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Introduction to Bioinformatics
databases: Nucleic Acid
Databases





Dinesh
Gupta



ICGEB

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Biological databases: why?

•
Need for storing and communicating
large datasets has grown


•
Make biological data available to
scientists.


•
To make biological data available in
computer
-
readable form.



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Different classifications of
databases

•
Type of data

–
nucleotide sequences

–
protein sequences

–
proteins sequence patterns or motifs

–
macromolecular 3D structure

–
gene expression data

–
metabolic pathways


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Different classifications of databases….

•
Primary or derived databases

–
Primary databases: experimental results
directly into database

–
Secondary databases: results of analysis of
primary databases

–
Aggregate of many databases

•
Links to other data items

•
Combination of data

•
Consolidation of data


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Different classifications of databases….

•
Technical design

–
Flat
-
files

–
Relational database (SQL)

–
Exchange/publication technologies (FTP,
HTML, CORBA, XML,...)


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Different classifications of databases….

•
Availability

–
Publicly available, no restrictions

–
Available, but with copyright

–
Accessible, but not downloadable

–
Academic, but not freely available

–
Proprietary, commercial; possibly free for
academics


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Where do I get DB of my interest ?


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http://www3.oup.co.uk/nar/database/c/


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Nucleotide sequence databases


•
EMBL, GenBank, and DDBJ are the
three
primary nucleotide sequence
databases


•
EMBL
www.ebi.ac.uk/embl/


•
GenBank
www.ncbi.nlm.nih.gov/Genbank/


•
DDBJ
www.ddbj.nig.ac.jp


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Genbank

•
An annotated collection of all publicly
available nucleotide and proteins


•
Set up in 1979 at the LANL (Los Alamos).


•
Maintained since 1992 NCBI (Bethesda).


•
http://www.ncbi.nlm.nih.gov


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EMBL Nucleotide Sequence
Database


•
An annotated collection of all publicly available
nucleotide and protein sequences


•
Created in 1980 at the
European Molecular
Biology Laboratory

in Heidelberg.


•
Maintained since 1994 by EBI
-

Cambridge.


•
http://www.ebi.ac.uk/embl.html


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http://www3.ebi.ac.uk/Services/DBStats/


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DDBJ
–
DNA Data Bank of Japan

•
An annotated collection of all publicly available
nucleotide and protein sequences


•
Started, 1984 at the
National Institute of
Genetics

(NIG) in Mishima.


•
Still maintained in this institute a team led by
Takashi Gojobori.


•
http://www.ddbj.nig.ac.jp


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Other NCBI nucleic acids DBs

•
EST database:

A collection of expressed sequence tags, or short, single
-
pass sequence
reads from mRNA (cDNA).

•
GSS database
: A database of genome survey sequences, or short, single
-
pass genomic
sequences.


•
HomoloGene:

A gene homology tool that compares nucleotide sequences between pairs of
organisms in order to identify putative orthologs.

•
HTG database:

A collection of high
-
throughput genome sequences from large
-
scale
genome sequencing centers, including unfinished and finished sequences.


•
SNPs database:

A central repository for both single
-
base nucleotide substitutions and
short deletion and insertion polymorphisms.

•
RefSeq:

A database of non
-
redundant reference sequences standards, including genomic
DNA contigs, mRNAs, and proteins for known genes. Multiple collaborations, both within
NCBI and with external groups, supports data
-
gathering efforts.


•
STS database:

A database of sequence tagged sites, or short sequences that are
operationally unique in the genome.

•
UniSTS:

A unified, non
-
redundant view of sequence tagged sites (STSs).

•
UniGene:

A collection of ESTs and full
-
length mRNA sequences organized into clusters,
each representing a unique known or putative human gene annotated with mapping and
expression information and cross
-
references to other sources.

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Sequence submission

•
Data mainly direct submissions from the
authors.

•
Submissions through the Internet:

–
Web forms.

–
Email.

•
Sequences shared/exchanged between
the 3 centers on a daily basis:

–
The sequence content of the banks is
identical.

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Derived databases

•
CUTG Codon usage tabulated from GenBank
http://www.kazusa.or.jp/codon/

•
Genetic Codes Deviations from the standard genetic code in various
organisms and organelles
http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c

•
TIGR Gene Indices Organism
-
specific databases of EST and gene
sequences
http://www.tigr.org/tdb/tgi.shtml

•
UniGene Unified clusters of ESTs and full
-
length mRNA sequences
http://www.ncbi.nlm.nih.gov/UniGene/

•
ASAP Alternative spliced isoforms
http://www.bioinformatics.ucla.edu/ASAP

•
Intronerator Introns and alternative splicing in C.elegans and
C.briggsae
http://www.cse.ucsc.edu/~kent/intronerator/

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Nucleic acid structure

databases

•
NDB Nucleic acid
-
containing structures
http://ndbserver.rutgers.edu/


•
NTDB Thermodynamic data for nucleic acids
http://ntdb.chem.cuhk.edu.hk/


•
RNABase RNA
-
containing structures from PDB and
NDB
http://www.rnabase.org/


•
SCOR Structural classification of RNA: RNA motifs by
structure, function and tertiary interactions

•
http://scor.lbl.gov/


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Database searching tips

•
Look for links to
Help

or Examples

•
Try
Boolean

searches

•
Be careful with UK/US
spelling

differences

–

leukaemia vs leukemia

–

haemoglobin vs hemoglobin

–

colour vs color


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Exercises

•
Study

the

statistics

of

the

three

primary

nucleic

acid

databases
:

Are

they

matching

?

•
Look

for

a

gene

of

your

interest

in

the

three

primary

nucleic

acid

databases
:

compare

the

information

given

in

each

one

of

them
.

•
Read

NAR

DB

paper

and

NAR

DB

index

site
:

search

for

different

nucleic

acid

databases

based

on

different

search

terms
.

•
Self study:

–
http://www3.oup.co.uk/nar/database/c/

–
Download NAR database paper (NARDB2004) from:
ftp://cbag.sc.mahidol.ac.th/pub/Course_Materials/dinesh