常用生物信息学数据库和分析工具网址

1、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.htmlPlant genome dababase tutorial/pgdic生物信息学机NCBI/International Nucleotide Sequence Database Collaboration./collab/EBI http:/www.ebi.ac.u

2、k/USDA/Sanger Centrehttp:/genomic.sanger.ac.uk/北京大学生物信息学中心数据库信息发布及其它GenBank Release Notes/genbank/gbrel.txtdbEST summary report/dbEST/dbESTsummarv.htmlEMBL release notes http:/www.bio.unizh.ch/db/docu.html?data=emrelEukaryotic prom

3、oter database release noteshttp:/www.genome.ad.jp/dbget/dbget2.htmlKEGG release notes http:/www.genome.jp/kegg/docs/relnote.html核苷酸数据库GenBank/dbEST /dbEST/index.htmldbSTS/dbSTS/index.htmldbGSS /db

4、GSS/index.htmlGenome (NCBI)/entrez/query.fcgi?db=GenomedbSNP/SNP/HTGS /HTGS/UniGene/UniGene/EMBL核苷酸数据库 http:/www.ebi.ac.uk/emblGenome (EBI)http:/www.ebi.ac.uk/genomes/向EMBL数据库提交序列http:/www.ebi.ac.

5、uk/embl/Submission/webin.htmlDDBJ http:/www.ddbj.nig.ac.jp/启动子数据库Eukaryotic promoter databasehttp:/www.epd.isb-sib.ch/转录因子数据库FRANSFAChttp:/www.gene-TFD基因分类数据库Gene Ontology (GO)蛋白质数据库SWISS-PROT或TrEMBL http:/www.ebi.ac.uk/swissprot/http:/www.expasy.ch/sprot/

6、 PIR /pir/PRFhttp:/www.prf.or.jp/PDBSTRhttp:/www.genome.ad.jp/dbget-bin/www_bfind?pdbstrPrositehttp:/www.expasy.ch/sprot/prosite.html结构数据库PDB/pdbNDB /NDB/ndb.html/DNA-Binding Protein

7、 Database /NDB/structure-finder/dnabind/index.htmlNMR Nucleic Acids Database/NDB/structure-finder/nmr/index.htmlProtein Plus Database/NDB/structure-finder/protein/index.htmlSwiss 3Dimage http:/www.expasy.ch/sw3d/SCOP ht

8、tp:/scop.mrc-lmb.cam.ac.uk/scop/CATHhttp:/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/Enzyme Nomenclature Database http:/expasy.hcuge.ch/sprot/enzyme.htmlProtein Kinase Resource (PKR)/kinases/LIGAND http:/www.genome.ad.jp/dbget/ligand.htmlWIT http:/w

9、/WIT/EcoCyc http:/ecocyc.PangeaSUM-BBD /umbbd/多种代谢路径数据库/stc-95/ResTools/biotools/biotools8.html基因调控路径数据库(TRANSPATH)http:/transfac.gbf.de基因组数据库禾本科比较基因组GrainGeneBotanical DatabasesBotanical Datahttp:/ww

10、/calflora/batanical.html日本水稻基因组 (RGP)http:/rgp.dna.affrc.go.jp水稻物理图谱/projects/rice/fpc华大水稻基因组框架图欧洲水稻测序（第12染色体）s.frMaize genomeBarley genome/Research/barley/nabgmp.htmForage grasses

11、 genomes//Topics/Species/Grasses/Triticum genomes/index.shtmlArabidopsis genomeSoyBase4Alfalfa genomeCotton genomeGlycine

12、 max genome/PlantGDB/glycine_max.html/PlantGDBC. elegans genome藻类（Chlamydomonas）基因组/chlamy_genome粘菌（Dictyostelium）基因组Animal genomes (ArkDB)FlyBasehttp:/

13、/Mouse Genome Informatics /Saccharomyces Genome Database/多种基因组数据库http:/www.hgmp.mrc.ac.uk/GenomeWeb文献数据库PubMed /PubMed/OMIM/Omim/Agricola /ag98/Rice

14、Genetics Newsletter/newsletters/rice_geneticsProceedings of the National Academy of Sciences USA (PNAS)关键词为基础的数据库检索Entrez /Entrez/Entrez Nucleotide Sequence Search /Entrez/nucleotide.htmlEntrez Protein Sequen

15、ce Search /Entrez/protein.htmlSequence Retrieval System, Singapore .sg:80/srs5/Sequence Retrieval System, US :80/srs/srscSequence Retrieval System, UK http:/srs.ebi.ac.uk/GetEntry Nucleotide & Protein Sequence Searchhttp:/ftp2

16、.ddbj.nig.ac.jp:8000/getstart-e.htmlDatabase Search with Key Words http:/ftp2.ddbj.nig.ac.jp:8080/dbsearch-e-new.htmlDBGET/LinkDB http:/www.genome.ad.jp/dbget/dbget2.html序列为基础的数据库检索BLAST /BLAST/FASTA http:/www.ebi.ac.uk/fasta33/index.htmlBLITZ http:/www2.ebi.ac.uk/bicsw/SSe

17、arch rs.fr/bin/ssearch-guess.cgiElectronic PCR/STS/Proteome analysishttp:/www.ebi.ac.uk/proteome/多序列分析Clustal multiple sequence alignment:9331/multi-align/Options/clustalw. htmlBCM:9331/multi-align/multi-align.htmlEBI Cl

18、ustalW analysishttp:/www.ebi.ac.uk系谱分析PAUP /PAUP/EBI ClustalW analysishttp:/www.ebi.ac.ukGCG package PHYLIP /phylip.htmlMEGA/METREE /imegHennig86 /mes/hennig/software.htmlGAMBIT /

19、mcdbio/Faculty/Lake/Research/Programs/MacClade /macclade/macclade.htmlPhylogenetic analysis/stc-95/ResTools/biotools/biotools2.htmlClustalXftp:/ftp-igbmc.u-strasbg.fr/pub/ClustalXMEGA基因结构预测分析GENSCAN /GENSCAN.htmlhttp:/bioweb.pasteur.fr/s

20、eqanal/interfaces/genscan-simple.htmlhttp:/bioweb.pasteur.frGeneFinderhttp:/genomic.sanger.ac.uk/gf/gf.shtmlGene Feature Searches :9331/Grail /Grail-1.3/GrailEXP/grailexp/GeneMark /GeneMark/eukhmm.c

21、gi/GeneMark/hmmchoice.htmlVeil/labs/compbio/veil.htmlAAT /aat.htmlGENEID http:/www.imim.es/GeneIdentification/Geneid/geneid_input.htmlGenlang /sdong/genlang_home.htmlGeneParser http:/beagle.colorad

22、/eesnyder/GeneParser.htmlGlimmer/labs/compbio/glimmer.htmlMZEF /genefinderProcrustes/software/procrustes/基因分类GO Annotator/gofigure蛋白质结构预测分析Expasy http:/www.expasy.ch/CBShttp:/www.cbs.dtu.dkPredicting protein s

23、econdary structure :9331/pssprediction/pssp.htmlPredicting protein 3D Structures http:/dove.embl-heidelberg.de/3D/Predicting protein structures :9331/seq-search/struc-predict.html其它分析工具和软件Putative DNA Sequencing Errors Check http:/www.bork.embl-h

24、eidelberg.de/Frame/MatInspector http:/www.gsf.de/cgi-bin/matsearch.plFastM http:/www.gsf.de/cgi-bin/fastm.plWeb Signal Scan http:/www.dna.affrc.go.jp/htdocs/sigscan/signal.htmlBCM Search Launcher :9331/seq-util/seq-util.htmlWebcutter Translate DNA to protein http:/www.expasy.ch/tools/dna.htmlABIM http:/