常见生物信息学网站

用生物信息学数据库和分析工具网址

数据库

因特网网址

网上生物信息学教程　 EMBL biocomputing tutorials　

http://www.bio.cam.ac.uk/Embnetut/Gcg/index.html Plant genome dababase tutorial

http://www.nal.usda.gov/pgdic 　

生物信息学机构　

NCBI

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

International Nucleotide Sequence Database Collaboration.

http://www.ncbi.nlm.nih.gov/collab/ EBI

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

http://www.nal.usda.gov/ Sanger Centre

http://genomic.sanger.ac.uk/ 北京大学生物信息学中心

http://www.cbi.pku.edu.cn 　

数据库信息发布及其它　

GenBank Release Notes

ftp://ncbi.nlm.nih.gov/genbank/gbrel.txt

dbEST summary report

http://www.ncbi.nlm.nih.gov/dbEST/dbESTsummarv.html

EMBL release notes　　　

http://www.genome.ad.jp/dbget-bin/show man?embl

DDBJ release notes　　　

http://www.ddbj.nig.ac.jp/ddbjnew/ddbj relnote.html

Eukaryotic promoter database release notes

http://www.genome.ad.jp/dbget/dbget2.html

SwissProt release notes　　　

http://www.genome.ad.jp/dbget-bin/show man?swissprot

PIR release notes　

http://www.genome.ad.jp/dbget-bin/show man?pir

PRF release notes

http://www.genome.ad.jp/dbget-bin/show man?prf

PDBSTR release notes　　　

http://www.genome.ad.jp/dbget-bin/show man?pdbstr

Prosite release notes　　　

http://www.genome.ad.jp/dbget-bin/show man?prosite

PDB release notes　　　

http://www.genome.ad.jp/dbget-bin/show man?pdb

KEGG release notes　　　

http://www.genome.ad.jp/dbget-bin/show man?pathway 　

核苷酸数据库　

GenBank

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

dbEST

http://www.ncbi.nlm.nih.gov/dbEST/index.html

dbSTS

http://www.ncbi.nlm.nih.gov/dbSTS/index.html dbGSS

http://www2.ncbi.nlm.nih.gov/dbGSS/index.html

Genome (NCBI)

http://www.ncbi.nlm.nih.gov/Entrez/Genome/org.html

dbSNP

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

HTGS

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

UniGene

http://www.ncbi.nlm.nih.gov/UniGene/ EMBL核苷酸数据库　　　

http://www.ebi.ac.uk/embl Genome (EBI)

http://www.ebi.ac.uk/genomes/ 向EMBL数据库提交序列

http://www.ebi.ac.uk/embl/Submission/webin.html DDBJ　　

http://www.ddbj.nig.ac.jp/ Plant R gene database

http://www.ncgr.org/rgenes 　 　

启动子数据库　

Eukaryotic promoter database

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

http://www.genome.ad.jp/dbget/dbget2.html 　

转录因子数据库　 FRANSFAC

http://transfac.gbf.de ooTFD

http://www.ifti.org 　 蛋白质数据库　 SWISS-PROT或TrEMBL　　　

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

http://www.expasy.ch/sprot/ PIR

http://www-nbrf.georgetown.edu/pir/ PRF　　　

http://www.prf.or.jp/ PDBSTR

http://www.genome.ad.jp/dbget-bin/www bfind?pdbstr-today Prosite　　

http://www.expasy.ch/sprot/prosite.html 　

结构数据库　 PDB　　　

http://www.rcsb.org/pdb

http://www.pdb.org NDB　　　

http://ndbserver.rutgers.edu/NDB/ndb.html

http://ndbserver.rutgers.edu/ DNA-Binding Protein Database

http://ndbserver.rutgers.edu/NDB/structure-finder/dnabind/index.html NMR Nucleic Acids Database

http://ndbserver.rutgers.edu/NDB/structure-finder/nmr/index.html Protein Plus Database

http://ndbserver.rutgers.edu/NDB/structure-finder/protein/index.html Swiss 3Dimage　　

http://www.expasy.ch/sw3d/ SCOP　　

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

http://www.biochem.ucl.ac.uk/bsm/cath/ 　 酶、代谢和调控路径数据库　 KEGG　

http://www.genome.ad.jp/kegg/kegg2.html Enzyme Nomenclature Database　　　

http://expasy.hcuge.ch/sprot/enzyme.html Protein Kinase Resource (PKR)

http://www.sdsc.edu/kinases/ LIGAND　　　

http://www.genome.ad.jp/dbget/ligand.html WIT　　　

http://www.cme.msu.edu/WIT/ EcoCyc　

http://ecocyc.PangeaSystems.com/ecocyc/ UM-BBD　　　

http://www.labmed.umn.edu/umbbd/

多种代谢路径数据库

http://www.unl.edu/stc-95/ResTools/biotools/biotools8.html

基因调控路径数据库(TRANSPATH)

http://transfac.gbf.de 　

基因组数据库　 日本水稻基因组数据库(RGP)

http://rgp.dna.affrc.go.jp 华大水稻基因组框架图

http://www.genomics.org.cn 欧洲水稻测序（第12染色体）

http://www.genoscope.cns.fr 拟南芥基因组数据库

http://www.arabidopsis.org USDA Database　

http://www.nal.usda.gov/ Demeter’s Genomes

http://genome.cornell.edu RiceGenes　　

http://genome.cornell.edu/cgi-bin/WebAce/webace?db=ricegenes RiceBlastDB　

http://genome.cornell.edu/cgi-bin/WebAce/webace?db=riceblastdb FlyBase

http://flybase.bio.indiana.edu/.bin/fbidq.html?FBgn0003075 Mouse Genome Informatics

http://www.informatics.jax.org/bin/query_accession?id=MGI:97555 Saccharomyces Genome Database

http://genome-www.stanford.edu/cgi-bin/dbrun/SacchDB?find+Locus+%22PGK1%22 多种基因组数据库

http://www.hgmp.mrc.ac.uk/GenomeWeb 　 文献数据库　 PubMed

http://www.ncbi.nlm.nih.gov/PubMed/ OMIM

http://www.ncbi.nlm.nih.gov/Omim/ Agricola

http://www.nal.usda.gov/ag98/ 　

关键词为基础的数据库检索　 Entrez　　

http://www.ncbi.nlm.nih.gov/Entrez/ Entrez Nucleotide Sequence Search　

http://www.ncbi.nlm.nih.gov/Entrez/nucleotide.html Entrez Protein Sequence Search　

http://www.ncbi.nlm.nih.gov/Entrez/protein.html Batch Entrez　

http://www.ncbi.nlm.nih.gov/Entrez/batch.html Sequence Retrieval System, India

http://bioinfo.ernet.in:80/srs5/ Sequence Retrieval System, Singapore　　　

http://www.bic.nus.edu.sg:80/srs5/ Sequence Retrieval System, US　

http://iubio.bio.indiana.edu:80/srs/srsc Sequence Retrieval System, UK　

http://srs.ebi.ac.uk/ GetEntry Nucleotide & Protein Sequence Search

http://ftp2.ddbj.nig.ac.jp:8000/getstart-e.html Database Search with Key Words　

http://ftp2.ddbj.nig.ac.jp:8080/dbsearch-e-new.html DBGET/LinkDB　

http://www.genome.ad.jp/dbget/dbget2.html 　

序列为基础的数据库检索　 BLAST　

http://www.ncbi.nlm.nih.gov/BLAST/ FASTA　

http://www2.ebi.ac.uk/fasta3/ BLITZ　　

http://www2.ebi.ac.uk/bicsw/ SSearch

http://www2.igh.cnrs.fr/bin/ssearch-guess.cgi Electronic PCR

http://www.ncbi.nlm.nih.gov/STS/ Proteome analysis

http://www.ebi.ac.uk/proteome/ 　

多序列分析　 Clustal multiple sequence alignment

http://dot.imgen.bcm.tmc.edu:9331/multi-align/Options/clustalw. html BCM

http://dot.imgen.bcm.tmc.edu:9331/multi-align/multi-align.html EBI ClustalW analysis

http://www.ebi.ac.uk 　 系谱分析　 PAUP　　

http://onyx.si.edu/PAUP/ EBI ClustalW analysis

http://www.ebi.ac.uk GCG package　　　

http://www.gcg.com/ PHYLIP

http://evolution.genetics.washington.edu/phylip.html MEGA/METREE

http://www.bio.psu.edu/imeg Hennig86　　　

http://www.vims.edu/~mes/hennig/software.html GAMBIT

http://www.lifesci.ucla.edu/mcdbio/Faculty/Lake/Research/Programs/ MacClade　　

http://phylogeny.arizona.edu/macclade/macclade.html Phylogenetic analysis

http://www.unl.edu/stc-95/ResTools/biotools/biotools2.html 　

基因结构预测分析　 GENSCAN　

http://genes.mit.edu/GENSCAN.html GeneFinder

http://genomic.sanger.ac.uk/gf/gf.shtml

http://www.softberry.com/nucleo.html Gene Feature Searches　　　

http://dot.imgen.bcm.tmc.edu:9331/ Grail　　　

http://compbio.ornl.gov/Grail-1.3/ GrailEXP

http://grail.lsd.ornl.gov/grailexp/ GeneMark

http://genemark.biology.gatech.edu/GeneMark/hmmchoice.html Veil　

http://www.cs.jhu.edu/labs/compbio/veil.html AAT　　　

http://genome.cs.mtu.edu/aat.html GENEID

http://www.imim.es/GeneIdentification/Geneid/geneid_input.html Genlang　

http://cbil.humgen.upenn.edu/~sdong/genlang_home.html GeneParser　

http://beagle.colorado.edu/~eesnyder/GeneParser.html Glimmer

http://www.cs.jhu.edu/labs/compbio/glimmer.html MZEF　　

http://www.cshl.org/genefinder Procrustes　　

http://www-hto.usc.edu/software/procrustes/ 　

蛋白质结构预测分析　 Expasy　

http://www.expasy.ch/ Predicting protein secondary structure

http://dot.imgen.bcm.tmc.edu:9331/pssprediction/pssp.html Predicting protein 3D Structures　　　

http://dove.embl-heidelberg.de/3D/ Predicting protein structures

http://dot.imgen.bcm.tmc.edu:9331/seq-search/struc-predict.html 　

其它分析工具和软件　 Putative DNA Sequencing Errors Check　　

http://www.bork.embl-heidelberg.de/Frame/ MatInspector

http://www.gsf.de/cgi-bin/matsearch.pl FastM　　

http://www.gsf.de/cgi-bin/fastm.pl Web Signal Scan　

http://www.dna.affrc.go.jp/htdocs/sigscan/signal.html BCM Search Launcher　　　

http://dot.imgen.bcm.tmc.edu:9331/seq-util/seq-util.html Webcutter　　

http://www.firstmarket.com/cutter/cut2.html Translate DNA to protein　　

http://www.expasy.ch/tools/dna.html ABIM　　

http://www-biol.univ-mrs.fr/english/logligne.html sequence motifs: 　 Pfam　　　

http://www.sanger.ac.uk/Pfam/

http://pfam.wustl.edu/ ProDom

http://protein.toulouse.inra.fr/prodom.html PRINTS

http://www.biochem.ucl.ac.uk/bsm/dbbrowser/PRINTS/ 　

其它　 多种数据库、分析工具和生物信息学机构

http://www.unl.edu/stc-95/Restools/biotools 多种数据库和分析工具

http://www.ebi.ac.uk/Tools/ Comparative sequence analysis

http://www.bork.embl-heidelberg.de/ 　 功能基因组分析　 Transcription profiling technologies

http://www.ncbi.nlm.nih.gov/ncicgap/expression_tech_info.html Protocols for cDNA array technology　　

http://cmgm.stanford.edu/pbrown/array.html Data management and analysis of gene expression arrays

http://www.nhgri.nih.gov/DIR/LCG/15k/HTML/

Examples of commercially available filter arrays: 　 GeneFiltersTM (Research Genetics)　　　

http://www.resgen.com Gene Discovery Arrays (Genome Systems)　　　

http://www.genomesystems.com AtlasTM Arrays (CLONTECH)　　

http://www.clontech.com