הקיטמרופניאויבל אובמ
...
שדח דמימל היגולויבה תא תחקל
רמוש ינב
,
רבמבונ
2005
Exponential Growth Rate
Over the last two decades, nucleic acid data has accumulated at the EMBL
database at an exponential rate, currently totaling ~110 Gbases, related from
62M entries.
~
200
,
000
Protein Entries
Currently stored in the
UniProt database, with
70
M amino acids.
ERK2 MAP Kinase
The whole genome of over
1500
viruses and
775
bacteria has been completely sequenced or is in
progress…
Haemophilus influenza
Bacteriophage T
4
Salmonella sp.
…as well as some 400 eukaryotic genomes
of which 135 are of parasites, fungi and other lower forms.
Trypanosoma brucei
Schizosaccharomyces pombe
Plasmodium falciparum
Leishmania major
More than 500 organelle genomes are in the databases
Mitochondrion
3
D CAT
Chloroplast
Mitochondria
About
80
plants are being genome/EST sequenced or
genetically mapped
Arabidopsis thaliana
There are currently ~
170
genome projects
of Metazoa
3.2
Gb
~
30
,
000
genes.
"
עדי לש רגאמ לע תולעב
,
ןטק אל רשוא והז
"
סטרקוס
"
תויצרופורפמ תאצל ךירצ אל
םיינתמה לע שארה םע ראשיהל ךירצו
"
יחרזמ ןולא
Same Size Genome ~3Gb
About same number of genes (
30
,
000
)
Same gene contents
85
-
90%
similarity between genes
(up to
98
% similarity with apes)
Genes & Development Vol.
14
, No.
20
, pp.
2551
-
2569
, October
15
,
2000
The Basis for Bioinformatics
From Sequence to Biology
1460 1470 1480 1490 1500
AF
3071
TGGGCAATTCCCAGAAATTAATGGCTATGAGTTCTTTTTTGATCAACTCA
:: ::::::: ::::::::::::: :::::::: : ::::::::::::
AF
0712
TGTGCAATTCAAAGAAATTAATGGCCATGAGTTCCTATTTGATCAACTCC
180 190 200 210 220
1510 1520 1530 1540 1550
AF
3071
AACTATGTCGACCCCAAGTTCCCTCCATGCGAGGAATATTCACAGAGCGA
:::::::: ::::: ::::: :: :: :::::::::::::: ::::::::
AF
0712
AACTATGTGGACCCTAAGTTTCCACCCTGCGAGGAATATTCCCAGAGCGA
230 240 250 260 270
1560 1570 1580 1590 1600
AF
3071
TTACCTACCCAGCGACCACTCGCCCGGGTACTACGCCGGCGGCCAGAGGC
::::::::::: ::::: :: : ::::: : ::: ::::::::
AF
0712
CTACCTACCCAGT
---
CACTCTCCGG
---
ACTACTACAGCGCCCAGAGGC
280 290 300 310
1610 1620 1630 1640 1650
AF
3071
GAGAGAGCAGCTTCCAGCCGGAGGCGGGCTTCGGGCGGCGCGCGGCGTGC
::: : ::::::: ::: :: :: : : ::: ::: :::
AF
0712
AAGACCCCTCGTTCCAGCATGAGTCGATCTACCACCAGCGGTCGGGCTGC
320 330 340 350 360
Human
Zebrafish
HoxB
4
local alignment
Local, Global, Multiple…
Elongation Factor
1
alpha
>gi|28558768|sp|P53601|A4_MACFA Amyloid beta A4 protein precursor (APP)
(ABPP) (Alzheimer's disease
amyloid protein homolog) [Contains: Soluble APP
-
alpha
(S
-
APP
-
alpha); Soluble APP
-
beta (S
-
APP
-
beta); C99;
Beta
-
amyloid protein 42 (Beta
-
APP42); Beta
-
amyloid
protein 40 (Beta
-
APP40); C83; P3(42); P3(40);
Gamma
-
CTF(59) (Gamma
-
secretase C
-
terminal fragment 59);
Gamma
-
CTF(57) (Gamma
-
secretase C
-
terminal fragment 57);
Gamma
-
CTF(50) (Gamma
-
secretase C
-
terminal fragment 50);
C31]
Length = 770
Score = 1277 bits (3305), Expect = 0.0
Identities = 642/752 (85%), Positives = 643/752 (85%)
Query: 19 EVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYP 78
EVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYP
Sbjct: 19 EVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYP 78
Query: 79 ELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKFLHQ 138
ELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKFLHQ
Sbjct: 79 ELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKFLHQ 138
Query: 139 ERMDVCETHLHWHTVAKETCSEKSTNLHDYGMLLPCGIDKFRGVEFVCCPLXXXXXXXXX 198
ERMDVCETHLHWHTVAKETCSEKSTNLHDYGMLLPCGIDKFRGVEFVCCPL
Sbjct: 139 ERMDVCETHLHWHTVAKETCSEKSTNLHDYGMLLPCGIDKFRGVEFVCCPLAEESDNVDS 198
Query: 199 XXXXXXXXXXWWGGADTDYADGSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 258
WWGGADTDYADGS
Sbjct: 199 ADAEEDDSDVWWGGADTDYADGSEDKVVEVAEEEEVAEVEEEEADDDEDDEDGDEVEEEA 258
Query: 259 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCSEQAETGPCRAMISRWYFDVTEGKCAP 318
CSEQAETGPCRAMISRWYFDVTEGKCAP
Sbjct: 259 EEPYEEATERTTSIATTTTTTTESVEEVVREVCSEQAETGPCRAMISRWYFDVTEGKCAP 318
SNP
RNA secondary structure prediction
TF Analysis
Gene Analysis
Genome Level Annotation
Genome Level Annotation
Chromosome
Slider
Focus Position
Focus Area
Overview
Chromosome Oriented
Genome Level Annotation
Focus Area
Detailed View
Genome Level Annotation
Focus Area
Basepair View
Genome Level Annotation
Gene Oriented
Protein properties
EX
33
inflammation related GPCR analysis
Protein properties
EX
33
inflammation related GPCR analysis
.
10
.
20
.
30
.
40
.
50
MWNSSDANFSCYHESVLGYRYVAVSWGVVVAVTGTVGNVLTLLALAIQPK
helix HHHHHHH
sheet E E EEEEEEEEEEEEEEE EEEE E
turns TT TTTTT TTTT TTT T
coil CC CCCC
.
60
.
70
.
80
.
90
.
100
LRTRFNLLIANLTLADLLYCTLLQPFSVDTYLHLHWRTGATFCRVFGLLL
helix HHHHHHHH H
sheet EE EEEEEE EEEEEEEE E EEEE EEEEEEEE
turns T TT T TTTTTTT
coil C
.
110
.
120
.
130
.
140
.
150
FASNSVSILTLCLIALGRYLLIAHPKLFPQVFSAKGIVLALVSTWVVGVA
helix HH HHHHH HHHHHH
sheet EEEEEEE EEEE EEE EEEEEEEEEEEEEE
turns T TT T
coil C C CC C
.
160
.
170
.
180
.
190
.
200
SFAPLWPIYILVPVVCTCSFDRIRGRPYTTILMGIYFVLGLSSVGIFYCL
helix
sheet EEEEEEEEEEEE EEEEEEEEEEEE EEEEEE
turns T TTTTTTT T TT
coil CCCC C CC CC
Secondary Structure Prediction
Garnier
Plotstructure
PredictProtein
3D Structure analysis
ID GATA_ZN_FINGER_
1
; PATTERN.
AC PS
00344
;
DT NOV
-
1990
(CREATED); NOV
-
1997
(DATA UPDATE); JUL
-
1998
(INFO UPDATE).
DE GATA
-
type zinc finger domain.
PA C
-
x
-
[DN]
-
C
-
x(
4
,
5
)
-
[ST]
-
x(
2
)
-
W
-
[HR]
-
[RK]
-
x(
3
)
-
[GN]
-
x(
3
,
4
)
-
C
-
N
-
[AS]
-
C.
NR /RELEASE=
41.18
,
131945
;
NR /TOTAL=
99
(
61
); /POSITIVE=
99
(
61
); /UNKNOWN=
0
(
0
); /FALSE_POS=
0
(
0
);
NR /FALSE_NEG=
14
; /PARTIAL=
0
;
CC /TAXO
-
RANGE=??E??; /MAX
-
REPEAT=
2
;
CC /SITE=
1
,zinc; /SITE=
4
,zinc; /SITE=
15
,zinc; /SITE=
18
,zinc;
DR O
13412
, AREA_ASPNG, T; O
13415
, AREA_ASPOR, T; P
17429
, AREA_EMENI, T;
Pattern and Motif Analysis
Protein Families
Pathway Analysis
Pathway Analysis
Protein
-
Protein interaction
Triclosan
-
FabI
Data Sources:
Yeast Two Hybrid system
Protein
-
Protein interaction
Data Sources:
Surface Plasmon Resonance
Triclosan
-
FabI
Protein
-
Protein interaction
Data Sources:
Natural Language Processing
DNA Microarray
& Expression Analysis
Cloning,
Restriction
& Mapping
PCR Design
Linguistics &
Information systems
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