NAR??

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NAR??

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Title: NAR??

1

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2
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3
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4
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5
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6
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7
(No Transcript)
8
NAR??

????(Nucleic Acids Research, NAR)(http//nar.oxf
ordjournals.org/)???1994??,???????????????
2000??,????????????????????????,??????????,?????
????????

9
(No Transcript)
10
NAR(Nucleic Acid Research)?????

???????(Nucleic Acid Sequence)
???????(Gene Expression)
?????????(Comparative genomics)
????????????(Gene Identification and Structure)

??????????(Genetic and physical maps)
??????(Genomic Databases)
?????????(Intermolecular interactions)
????????????(Metabolic Pathways and Cellular
Regulation)
?????(Mutation Databases)
?????(Pathology)

??????(Protein Databases)
????????(Protein sequence Motifs)
???????(Proteome Resources)
RNA?????(RNA Sequences)
?????(Structure)

13
??? ???????

???????????????
(1)???????????GenBank http//www.ncbi.nlm.nih.g
ov/Web/Genbank/index.html
(2)???????????EMBL
http//www.embl-heidelberg.de
(3)????????DDBJ
http//www.ddbj.nig.ac.jp/

14

??????????? (????????????,????bp)
15
??????????
16
Half day on the web,
saves you
half month in the lab.
- Alan Bleasby
17
NCBI?????
GenBank???
18
Search Human alternatively spliced mRNA sequences
GenBank Search
19
A sample GenBank record.
20
Saving search results.
21
Saving large result sets Batch Entrez
22
GenBank????
Accession number
????
????
Definition ??
GI number
???
23
GenBank?????
24
FASTA??
25
EMBL???

21 Mar 2003 37,943,364,438 bases in 24,353,128 records.
26

EMBL????????(??Gigabases) (EST-Expressed sequence tags STS-sequence tagged sites) (??http//www3.ebi.ac.uk/Services/DBStats/)
27
EMBL??????????????????????,????????????
EMBL?????????ASCII???????, ???????????????????
????????????????, ????????????????(annotation)
ID????????,????????,?????
AC????? XX?????? DT?????????
DE?????? KW????? OG??????? OS????????
OC?????????? RN????????? RP????????? RA
????????? RT????????? RL????????? RC?????
???? RX?DR????????? FH ??????? FT?????
(1)Feature Key,?????????????
(2)Location,????????????? (3)Qualifiers,?????
????????
???????????,?SQ??????? ????????//?
28
????
(1)??????
(2)??Authorin??
(3)????WWW???????????
29
??EMBL
(1)CD-ROM??
(2)ftp???
(3)Gopher???
(4)WWW???
????????????
30
EMBL??????????????(??3W???)
(1)????
????????????????(?X58929) ?????(?SCARGC)?????
??????????,??????????HTML??????? ???????????MEDLI
NE?????,????????????????????MEDLINE?? ???????????
??????,????????
31
?? ????J00231????????????????
DR SWISS-PROTP01860GC3_HUMAN
(2)???????
3W?????????FastA??????????? FastA?????????????????
?????
32
??????(GDB)
???????????????
??GDB????????????
(1)??????? ????????PCR????????????????????
EST??????contigs????
(2)???????, ??????????????????????contig
???????,?????????????????
(3)?????????, ????????????,???????????
33
?????????
34
???????????? ???????? MGD (http//www.informatic
s.jax.org/) ???????? SGD (http//genome-www.stan
ford.edu/Saccharomyces/)
35
????????Ensembl
Ensembl (http//www.ensembl.org/)

Ensembl????????????DNA??,???????????????
?????????,??????????????
????
???????
?????GenScan?????
?????
???????(SNP)??????

36
Ensembl ??????
37

Ensembl????????
???????
?BLAST?????????
????????????????
??????????????????? ????
???????

38
(No Transcript)
39
???9???????????????
40
Genomic Data

Entrez Genome (http//www.ncbi.nlm.nih.gov/entrez/
query.fcgi?dbGenome)
TIGR Genome (http//www.tigr.org/tdb/)
GDB (http//gdbwww.gdb.org/)

41
Genomic map

Entrez Genome viewer (http//www.ncbi.nlm.nih.gov/
cgi-bin/Entrez/map_search)
GDB Mapviewer (http//www.gdb.org/gdb-bin/genera/g
enera/hgd/Map?!modequery)
Ensembl genome browser (http//www.ensembl.org/)

42
Morbid /Disease
Genes
Ideogram
43
?????????dbEST
EST(Expressed Sequence Tags)???????????????????
,EST????????????90?
DbEST (http//www.ncbi.nlm.nih.gov/dbEST/) ?GenBan
k?????,???????????EST?? ?????????,????????????????
? mRNA???
??EST???
WEB???email
dbEST???
FTP
44
Gene Expression Data

NCBI dbEST (http//www.ncbi.nlm.nih.gov/dbEST/)
Stanford Microarray Database (http//genome-www5.s
tanford.edu/MicroArray/SMD/)
Incyte LifeSeq Database (http//www.incyte.com/seq
uence/index.shtml)

45
?????????dbSTS
STS(Sequence Tagged Sites)??????? dbSTS(http//ww
w.ncbi.nlm.nih.gov/dbSTS/) ?NCBI??????,??????????(
STS) ????????? ????BLAST??STS???
46
?????????UniGene
UniGene( http//www.ncbi.nlm.nih.gov/UniGene/) ???
?GenBank??????????,?? ????????????
??UniGene??? ?????????????,??????????,
??????????????? ?????????,??????EST???
??,UniGene??????????????????, ??????????EST???
47
??? ????????
48
Primary Structure Database

Protein Information Resource, PIR
(http//pir.georgetown.edu)
SWISS-PORT (http//www/expasy.ch/sprot/)
TrEMBL (http//www.ebi.ac.uk/trembl/)
OWL (http//www.bioinf.man.ac.uk/dbbrowser/OWL/),
composite of SWISS-PROT, PIR, GenBank and NRL-3D.

49
Properties of PIR-PSD and Swiss-Prot
50
PIR(Protein Information Resource)

??
?????????????????,?????????????
???????????????????????????
???????????,??99????????????,??????????????????

???????????,PIR???????
(1)???????????????????
(2)???????????
(3)??????????????,????????????????
(4)??????????????

52
PIR??????????? ????????????, ?????????????? ?
???????????, ??BLAST?FastA?? ?????????????? ????
?????????, ?????????????? ???????
53
??????
54
SWISS-PROT
SWISS-PROT (http//www.expasy.ch/sprot/sprot-top.h
tml) ???????????????????,????? ?????????
SWISS-PROT??????????? (1)?????????????? (2)?????
??PIR???????? (3)???????? (4)????????????????
SWISS-PROT????????
55
1)?? ?SWISS-PROT?,??????????????? ?????? ????????
??????(??????????) ???? (A)????????
(B)????? (C)??????,???????ATP?????
(D)???????? (E)????????,?????????????
(F)?????????? (G)??????????????
(H)??????????
56
2)????

??????????,???????????
??????????????,???????????????

3)?????????
????????,?????????????????,???????????????
???????? ?EMBL??????????,
?PROSITE????????, ???????????PDB???? ?
57

??????
(a)??????
(b) ??Authorin??
(c)WWW???
??SWISS-PROT
(a)CD-ROM??
(b)ftp???
(c)Gopher???
(d)WWW???(SRS)
????????
(a)????
(b)?????????

58
TrEMBL
TrEMBL (http//www.ebi.ac.uk/trembl/index.html)
??SWISS-PROT????????? ???EMBL????????????(CDS)????
???????,???????????SWISS-PROT????? TrEMBL????? (
1)SP-TrEMBL(SWISS-PROT TrEMBL) ?????????SWISS-PROT
???,???SP-TrEMBL ???????SWISS-PROT?
???? (2)REM-TrEMBL(REMaining TrEMBL) ?????????SWI
SS-PROT???,??????????????
59
???????UniProt
??Swiss-Prot TrEMBL PIR
?????????????,????BLAST???????,???????FTP ?????
60
UniProt??3??? (1)UniProt Knowledgebase(UniProt)
??????????????????????? (2)UniProt
Non-redundant Reference(UniRef)???
??????????????????? ???????? (3)UniProt
Archive(UniParc) ???,?????????????
61
Secondary Structure Database

PROSITE (http//www.expasy.org/prosite/)
Motif database by Swiss Institute of
Bioinformatics.
Pfam (http//pfam.wustl.edu/)
High-quality protein domain family database based
on HMMs by Sanger Center.
InterproScan (http//www.ebi.ac.uk/interpro/scan.h
tml)
Integrated system of pattern(domain,motif) from
SWISS-PROT,TrEMBL,PROSITE,PRINTS,PFAM etc. by EBI.

62
(No Transcript)
63
InterProScan result
64
The Protein Folding Problem
65
Protein Folding Problem(Sequence 3D Structure)

1 Protein folding is thermodynamically determined
(Anfinsens thermodynamic principle)
Protein Environment
2. Protein folding is a reaction imvolving other
interacting molecules
(Principle of molecular interactions)
Protein Chaperonins .

66
Tertiary Structure Database

Protein Data Bank, PDB (http//www.rcsb.org/pdb/)
Structural Classification of Proteins, SCOP
(http//scop.mrc-lmb.cam.ac.uk/scop/)
Class, Architecture, Topology, Homology, CATH
(http//www.biochem.ucl.ac.uk/bsm/cath_new/)

PDB(Protein Data Bank)
PDB???????(X??????,????NMR)??????????????

?????????(explicit sequence)
?PDB???,????SEQRES????????,?????????????????????
?????????(implicit sequence)
PDB?????????????,??????????????????

69
Customizing the PDB's SearchFields form
Search PDB
70
(No Transcript)
71
PDB?? ??
HEADER HYDROLASE
19-FEB-97 1ADZ TITLE THE
SOLUTION STRUCTURE OF THE SECOND KUNITZ DOMAIN OF
TITLE 2 TISSUE FACTOR PATHWAY
INHIBITOR, NMR, 30 STRUCTURES
COMPND MOL_ID 1
COMPND 2
MOLECULE TISSUE FACTOR PATHWAY INHIBITOR
?????? COMPND 8
BIOLOGICAL_UNIT MONOMER
SOURCE MOL_ID 1

?????? SOURCE 7 EXPRESSION_SYSTEM_PLASMID
PFLAG KEYWDS
HYDROLASE, INHIBITOR, COAGULATION
EXPDTA NMR, 30
STRUCTURES
AUTHOR M.J.M.BURGERING,L.P.M.ORBON
S
REVDAT 1 25-FEB-98 1ADZ 0
JRNL AUTH
M.J.BURGERING,L.P.ORBONS,A.VAN DER DOELEN,
?????? REMARK 1 REFERENCE 1

REMARK 1 AUTH M.T.STUBBS II
REMARK 1 TITL
STRUCTURAL ASPECTS OF FACTOR XA INHIBITION
?????? REMARK 999 SEQUENCE

REMARK 999 1ADZ SWS P10646 1 -
111 NOT IN ATOMS LIST REMARK 999 1ADZ
SWS P10646 183 - 304 NOT IN ATOMS
LIST REMARK 999 THE FIRST NINE RESIDUES
ARE NOT PART OF THE TFPI DOMAIN II
REMARK 999 SEQUENCE BUT ARE FROM THE PFLAG
PEPTIDE CLONING VECTOR. DBREF 1ADZ
1 71 SWS P10646 TFPI_HUMAN 112
182 SEQADV 1ADZ ASP 1 SWS
P10646 ILE 112 ENGINEERED
SEQADV 1ADZ TYR 2 SWS P10646 ILE
113 ENGINEERED SEQRES 1
71 ASP TYR LYS ASP ASP ASP ASP LYS LEU LYS PRO
ASP PHE SEQRES 2 71 CYS PHE LEU
GLU GLU ASP PRO GLY ILE CYS ARG GLY TYR
SEQRES 3 71 ILE THR ARG TYR PHE TYR ASN
ASN GLN THR LYS GLN CYS SEQRES 4
71 GLU ARG PHE LYS TYR GLY GLY CYS LEU GLY ASN
MET ASN SEQRES 5 71 ASN PHE GLU
THR LEU GLU GLU CYS LYS ASN ILE CYS GLU
SEQRES 6 71 ASP GLY PRO ASN GLY PHE
HELIX 1 1
ASP 12 PHE 15 5
4 HELIX 2 2 ASN 34 THR
36 5 3
HELIX 3 3 LEU 57 ILE 63 1
7 SHEET 1 A 2
ARG 29 ASN 33 0
SHEET 2 A 2 GLN 38 PHE
42 -1 N PHE 42 O ARG 29
CRYST1 1.000 1.000 1.000 90.00 90.00
90.00 P 1 1 ORIGX1
1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000
0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000
0.00000 SCALE1
1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000
0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000
0.00000
72
RasMol
View PDB flat-file
73
(No Transcript)
74
PDB Deposition

AutoDep (http//autodep.ebi.ac.uk/)
AutoDep input tool, ADIT (http//pdb.rutgers.edu/a
dit/)

75
MMDB(Molecular Modeling Database)

????MMDB ?(NCBI)???????????????Entrez?????,??????
??????????????????
?PDB??,?????????????????,MMDB?????????,???????????
??????????????? ?
?????????????????????????????

76
MMDB ????
77
DNAMAN

DNAMAN
http//www.lynnon.com/
Integrated System for Sequence Analysis

78
??? ?????????
1??????????dbSNP
(http//www3.ncbi.nlm.nih.gov/SNP/),

??????
??????SNPs(Single nucleotide polymorphisms)
SNPs????????????????????
??????????????,???????????????,????????SNPs?

79
?? GTTTGTGATT ACTTTGTAAA AACAGTGTAA TAAGTACTCA
CTAAAGGAAA TTTAGAAAAT GATAAGCTTA Aggccgggca
tggtgcctca tgcctgtaat cctagcactt tgggaggctg
aggtgggtgg atcacctgag ctcaggagtt ccagatcatc
ctggacaata tggtgaaacc ctgtctacgc ttaaaatacg R
aaattagccg ggcgtggtgg ggcatgcctg tggtctcagc
tactttggag actaaggtag aaggatcact tgaatcctgg
aggtggaggt tgcagagtga gccaatatcg tgccactgca
ctccagccta ggtgacagag gaagactctg tctcaaaaaa
aagaaaaTAA GGCCAGACAC GGGGGCTCAT GCTTGTAATC
RA/G
80
?????
81
2???????????SCOP

SCOP??? ( http//scop.mrc-lmb.cam.ac.uk/scop/)????
??????????????????????????,??????????PDB???????
SCOP????????????????????,????????????????PDB???,?
?,????,???????
????????????????,???????????????,????????????????
(1)???????????
(2)???????????,????????
(3)?????????

82
(No Transcript)
83
3???????????DSSP

DSSP(http//www.sander.embl-heidelberg.de/dssp/)
?????????????
?????????PDB?????????,??????????????????
????????????????????????????
????????,DSSP???????????????????

84
The DSSP code H alpha helix B residue in
isolated beta-bridge E extended strand,
participates in beta ladder G 3-helix (3/10
helix) I 5 helix (pi helix) T hydrogen
bonded turn S bend ?
85
4?????????????HSSP

HSSP(http//www.sander.embl-heidelberg.de/hssp/)
??????
?????PDB,????SWISS-PROT
??PDB????????,HSSP???????????????????,????????????
??????????
HSSP?????????????,??????????,????????????

86
From PDB
From Swiss-prot
??????
???? ? ????
87
5?OMIM
http//www.ncbi.nlm.nih.gov80/entrez/query.fcgi?d
bOMIM

OMIM (Online Mendelian Inheritance in
Man),?????????????????? ?
????????????????????????????????????
OMIM???????
???????????????????????????,????????????,?????????
????????????OMIM?????

88
?????
89
6?EPD

EPD( http//www.epd.isb-sib.ch/ )
???????????
???EMBL??????????????,???????????????????????????
??????

90
7?TRRD

TRRD?????????????????,???????????????????????????
???TRRD??????????,??????????-????
TRRD6.0??????????
(1)?????TRRDGENES
(2)?????TRRDLCR
(3)?????TRRDUNITS
(4)?????????TRRDSITES
(5)?????TRRDFACTORS
(6)?????TRRDEXP
(7)?????TRRDBIB

91
8?TRANSFAC

TRANSFAC (http//transfac.gbf.de/)????????????????
?????,?????????????
TRANSFAC??6???
(1)SITE???
(2)GENE???
(3)FACTOR???
(4)CELL???
(5)CLASS???
(6)MATRIX??

92
9?BODYMAP

BODYMAP (http//bodymap.ims.u-tokyo.ac.jp/)
?????????????????,????????????????????????????????
??????3??EST?
????????,????????????,?????mRNA???,????????,??????
?

93
10?PROSITE

PROSITE ( http//www.expasy.ch/prosite/)??????????
???,????????????????????????????????
PROSITE???????????????????????????????????????????
??????????????????
PROSITE????????????????????,?????????????????????

94
11?DBCat
(http//www.infobiogen.fr/services/dbcat/)

DBCat??????????????,????500?????????????,?????????
??????
DNA
RNA
???
???
??
?????
?????????,

95
DBCat????????
???? ?????
DNA 87
RNA 29
Protein 94
Genomic 58
Mapping 29
Protein structure 18
Literature 43
Miscellaneous 153
96
12?PubMed

PubMed(http//www.ncbi.nlm.nih.gov/)?NCBI?????????
???????,???MEDLINE?Pre-MEDLINE????????????????????
??????????Entrez?????PubMed??????????

97
Biochemical Pathway Data

WIT (http//wit.mcs.anl.gov/WIT2/)
The Kyoto Encyclopedia of Genes and Genomes, KEGG
(http//www.genome.ad.jp/kegg/)
PathDB (http//www.ncgr.org/pathdb/)

98
KEGG Pathway
Large Difference
Expression Percentage
Pathway Catalog
99
GO Tree

Gene Ontology Consortium (http//www.geneontology.
org/)

100
Gene Ontology
Percent of Genes
Functional Catalog
101
??? ?????

?????
?????
????
??????
????
???? O(n2)
???????????????
FastA
BLAST

102
FASTA?????
1?FASTA??
?????????????????
??s
?? 6
?? t
6 8 10 s -----A-A-T--- t
--A-A-T----- 3 5 7
?? 3
103

FASTP??????????????????????????,?????????????????
???????????k??(????k???,k-tup),???????,k1?2?
k???????????k?????????????,????????????????,??????
?

104

??????????
(1)???
????????k?????
(2)????
????????????????????????
?????k?????si?tj,?????i-j?

105
1 2 3 4 5 6 7 8 9 10 11 s H
A R F Y A A Q I V L
??? A 2,6,7 F 4 H 1 I 9 L 11 Q
8 R 3 V 10 Y 5
1 2 3 4 5 6 7 8 t V
D M A A Q I A
?? 9 -2 -3 2 2 -6
2 1 -2 3
2 -1
???? -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5
6 7 8 9 10 1 1 2 1 1 4 1
1
??????
106
????????? (1)???????? (2)????????????????? ????
??????????????k??????,???????????????????,????????
???,??????????????? ????5??????PAM????????,???????
??s???t????????? ????????????,????????????????????
??????????????????????,????????????????????,??????
????????????????????,??????????????(????????????)?
????
107
FastA??????FastA3???,??2??FastA3 ??????
? ? ?????? ?????
FastA DNA DNA
FastA ??? ???
FASTX FASTY DNA ???
TFastA ??? DNA
TFASTX TFASTY ??? DNA
FASTS TFASTS ??????? ???
FASTS TFASTS ??????? DNA
FASTF TFASTF ??????? ???
FASTF TFASTF ??????? DNA
FastA??
108
FastA????
109
2?BLAST

BLAST ????????????????????BLAST??????????FastA????
??,????????????,?????? ?
???????????????,BLAST?????,??????????????????

110
BLAST?????
????????????,???????????????
??
??S
??t
??
111

????????,BLAST??????????????????????S?????
??S???????,???????????????S??????
????????????????????S

112

???????????,BLAST????????,???????????????????
???????????,???????????????

113

BLAST???????????
(1)??????????,????????
(2)????
(3)????

114

?????????
?????w????????
?????????????T
??,w?T?????
????????????w?(??????)?4
????????????????????????
?????,?????????????
Hash table
?????
?????????????
?????????????????????????,?????

115

??DNA????
????????????w?????
????,??????2?(bit)??,4?????????
?????????????????????

116

BLAST??????????????
????????????,

117
BLAST ????
118
(No Transcript)
119

???????????????
4??? Vs. 20???
DNA??????????
????
??????DNA??????

120
3?VAST
http//www.ncbi.nlm.nih.gov/Structure/VAST/)

VAST?NCBI?????????,??????????????PDB?MMDB?????????
???
????????,VAST??????????????????,???????????????Cn3
D(Wang et al., 2000)??????????,????????????????,??
??????????????? ?

121

VAST????????
??,?????????,??????????????a???ß???
????????????????????????????????????????????,?????
????????,??????????????????,????????????????????
??,???????????????????????????

122
??? ?????

???????????????????,?????????????,??????????????
?? .
Entrez?SRS??????????
??????????????????????,???????????

123
1?Entrez
http//www.ncbi.nlm.nih.gov/gorf/gorf.html

???????
??NCBI?????????
????
?????
???????
?????
???????
??????????(OMIM)
Pubmed

124

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

Entrez????????
125

126
(No Transcript)
127
2. SRS

SRS(Sequence Retrieval System)?EMBL???????WEB?????
SRS?????????
??EMBL?EMBL_NEW?SwissProt?PIR??????
??????????,
?????????????Prosite???????ReBase?PDB???????NRL_3
D???????????EPD?E.coli ???ECD??????????ENZYME?????
?????SEQANALREF?,??????????????,???80?????
SRS??????????????????????

128
(No Transcript)
129
3?ExPASy

ExPASy (Expert Protein Analysis
System,http//www.expasy.org/) ???????????????????
??WWW???,??????????????
??
????????SWISS-PROT?TrEMBL
????????????PROSITE
2??3?????????????SWISS-2DPAGE?SWISS-3DIMAGE?

130
??? ????????GCG