常用生物信息学数据库和分析工具网址.docx

1、常用生物信息学数据库和分析工具网址常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EBI 自修课程http:/www.ebi.ac.uk/2canNCBI自修课程http:/www.ncbi.nlm.nih.gov/Education自修课程http:/lectures.molgen.mpg.de/online_lectures.html生物信息学常问的问题http:/bioinformatics.org/faq/生物信息学机构NCBIhttp:/www.ncbi.nlm.nih.gov/International Nucleotide Sequence Database

2、Collaboration.http:/www.ncbi.nlm.nih.gov/collab/EBI http:/www.ebi.ac.uk/USDAhttp:/www.nal.usda.gov/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 Notesftp:/ncbi.nlm.nih.gov/genbank/gbrel.txtdbEST summary reporthttp:/www.ncbi.nlm.nih.gov/dbEST/dbESTsummarv.htmlEMBL relea

3、se notes http:/www.genome.ad.jp/dbget-bin/show man?emblDDBJ release notes http:/www.ddbj.nig.ac.jp/ddbjnew/ddbj relnote.htmlEukaryotic promoter database release noteshttp:/www.genome.ad.jp/dbget/dbget2.htmlSwissProt release notes http:/www.genome.ad.jp/dbget-bin/show man?swissprotPIR release notes h

4、ttp:/www.genome.ad.jp/dbget-bin/show man?pirPRF release notes http:/www.genome.ad.jp/dbget-bin/show man?prfPDBSTR release notes http:/www.genome.ad.jp/dbget-bin/show man?pdbstrProsite release notes http:/www.genome.ad.jp/dbget-bin/show man?prositePDB release notes http:/www.genome.ad.jp/dbget-bin/sh

5、ow man?pdbKEGG release notes http:/www.genome.ad.jp/dbget-bin/show man?pathway核苷酸数据库GenBankhttp:/www.ncbi.nlm.nih.gov/dbEST http:/www.ncbi.nlm.nih.gov/dbEST/index.htmldbSTS http:/www.ncbi.nlm.nih.gov/dbSTS/index.htmldbGSS http:/www.ncbi.nlm.nih.gov/dbGSS/index.htmlGenome (NCBI)http:/www.ncbi.nlm.nih

6、.gov/entrez/query.fcgi?db=GenomedbSNP http:/www.ncbi.nlm.nih.gov/SNP/HTGShttp:/www.ncbi.nlm.nih.gov/HTGS/UniGenehttp:/www.ncbi.nlm.nih.gov/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.uk/embl/Submission/webin.htmlDDBJ http:/www.ddbj.

7、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.chhttp:/www.genome.ad.jp/dbget/dbget2.html转录因子数据库FRANSFAChttp:/transfac.gbf.deooTFDhttp:/www.ifti.org基因注释数据库RAP-DBhttp:/rapdb.lab.nig.ac.jp基因分类数据库Gene Ontology (GO)http:/www.geneontology

8、.org蛋白质数据库SWISS-PROT或TrEMBL http:/www.ebi.ac.uk/swissprot/http:/www.expasy.ch/sprot/PIRhttp:/pir.georgetown.eduPRF http:/www.kinasenet.org/pkr/Welcome.dohttp:/www.prf.or.jp/PDBSTRhttp:/www.genome.ad.jpProsite http:/www.expasy.org/prosite结构数据库PDB http:/www.rcsb.org/pdbhttp:/www.pdb.orgNDB http:/ndbse

9、rver.rutgers.edu/NDB/ndb.htmlhttp:/ndbserver.rutgers.edu/DNA-Binding Protein Database http:/ndbserver.rutgers.edu/NDB/structure-finder/dnabind/index.htmlNMR Nucleic Acids Databasehttp:/ndbserver.rutgers.edu/NDB/structure-finder/nmr/index.htmlProtein Plus Databasehttp:/ndbserver.rutgers.edu/NDB/struc

10、ture-finder/protein/index.htmlSwiss 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/Enzyme Nomenclature Database http:/expasy.hcuge.ch/sprot/enzyme.htmlProtein Kinase Resource (PKR)http:/ww

11、w.sdsc.edu/kinases/LIGAND http:/www.genome.ad.jp/dbget/ligand.htmlWIT http:/www.cme.msu.edu/WIT/EcoCyc http:/ecocyc.PangeaSUM-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基因组数据库禾本科比较基因组http:/www.gramene.

12、orgGrainGenehttp:/www.graingenes.orgBotanical Datahttp:/www.calflora.org/calflora/batanical.html日本水稻基因组 (RGP)http:/rgp.dna.affrc.go.jp水稻物理图谱http:/www.genome.clemson.edu/projects/rice/fpchttp:/www.genome.arizona.edu华大水稻基因组框架图欧洲水稻测序（第12染色体）s.frOryGenesDB（水稻插入突变体）http:/orygenesdb.cirad.frMaize genomeht

13、tp:/www.agron.missouri.eduBarley genomehttp:/www.css.orst.edu/Research/barley/nabgmp.htmForage grasses genomeshttp:/forages.orst.edu/http:/www.forages.css.orst.edu/Topics/Species/Grasses/Triticum genomeshttp:/wheat.pw.usda.gov/index.shtmlArabidopsis genomehttp:/www.arabidopsis.orgSoyBasehttp:/soybas

14、e.agron.iastate.eduAlfalfa genomehttp:/www.alfalfa.ksu.eduCotton genomehttp:/cottongenomecenter.ucdavis.eduGlycine max genomehttp:/www.zmdb.iastate.edu/PlantGDB/glycine_max.htmlhttp:/www.zmdb.iastate.edu/PlantGDBC. elegans genomehttp:/www.acedb.org藻类（Chlamydomonas）基因组http:/www.biology.duke.edu/chlam

15、y_genome粘菌（Dictyostelium）基因组http:/dictygenome.bcm.tmc.eduAnimal genomes (ArkDB)http:/www.thearkdb.orgFlyBasehttp:/flybase.bio.indiana.edu/.bin/fbidq.html?FBgn0003075Mouse Genome Informatics http:/www.informatics.jax.org/bin/query_accession?id=MGI:97555Saccharomyces Genome Databasehttp:/genome-www.st

16、anford.edu/cgi-bin/dbrun/SacchDB?find+Locus+%22PGK1%22多种基因组数据库http:/www.hgmp.mrc.ac.uk/GenomeWebRice Mutant Database文献数据库PubMed http:/www.ncbi.nlm.nih.gov/PubMed/OMIMhttp:/www.ncbi.nlm.nih.gov/Omim/Agricola http:/www.nal.usda.gov/ag98/Rice Genetics Newsletterhttp:/www.gramene.org/newsletters/rice_ge

17、neticsProceedings of the National Academy of Sciences USA (PNAS)http:/intl.pnas.org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.htmlEntrez Protein Sequence Search http:/www.ncbi.nlm.nih.gov/Entrez/protein.htmlBatc

18、h Entrez http:/www.ncbi.nlm.nih.gov/Entrez/batch.htmlSequence 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/srscSequence Retrieval System, UK http:/srs.ebi.

19、ac.uk/GetEntry Nucleotide & Protein Sequence Searchhttp:/ftp2.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/序列为基础的数据库检索BLAST http:/www.ncbi.nlm.nih.gov/BLAST/FASTA http:/www.ebi.ac.uk/fast

20、a33/index.htmlBLITZ http:/www2.ebi.ac.uk/bic_sw/SSearch rs.fr/bin/ssearch-guess.cgiElectronic PCRhttp:/www.ncbi.nlm.nih.gov/STS/Proteome analysishttp:/www.ebi.ac.uk/proteome/Global alignmenthttp:/genome.cs.mtu.edu多序列分析Clustal multiple sequence alignmenthttp:/dot.imgen.bcm.tmc.eduBCMhttp:/dot.imgen.b

21、cm.tmc.edu:9331/multi-align/multi-align.htmlEBI ClustalW http:/www.ebi.ac.uk/clustaw/index.htmlClustal multiple sequence alignmenthttp:/genome.cs.mtu.edu修饰对序列对位排列结果的格式（Boxshade）http:/www.ch.embnet.org/software/BOX_form.html系谱分析PAUP http:/onyx.si.edu/PAUP/EBI ClustalW analysishttp:/www.ebi.ac.ukGCG p

22、ackage PHYLIP http:/evolution.genetics.washington.edu/phylip.htmlMEGA/METREE http:/www.bio.psu.edu/imegHennig86 http:/www.vims.edu/mes/hennig/software.htmlGAMBIT http:/www.lifesci.ucla.edu/mcdbio/Faculty/Lake/Research/Programs/MacClade http:/phylogeny.arizona.edu/macclade/macclade.htmlPhylogenetic a

23、nalysishttp:/www.unl.edu/stc-95/ResTools/biotools/biotools2.htmlClustalXftp:/ftp-igbmc.u-strasbg.fr/pub/ClustalXMEGATreeViewhttp:/taxonomy.zoology.gla.ac.uk/rod/treeview.html基因结构预测分析GENSCAN http:/genes.mit.edu/GENSCAN.htmlhttp:/bioweb.pasteur.fr/seqanal/interfaces/genscan-simple.htmlhttp:/bioweb.pas

24、teur.frGeneFinderhttp:/www.bioscience.org/urllists/genefind.htmGene FindingGene Feature Searches http:/dot.imgen.bcm.tmc.eduGrailhttp:/compbio.ornl.gov/Grail-1.3GrailEXPhttp:/compbio.ornl.gov/grailexpGeneMark http:/opal.biology.gatech.edu/GeneMark/eukhmm.cgihttp:/genemark.biology.gatech.edu/GeneMark

25、/hmmchoice.htmlVeil http:/www.cs.jhu.edu/labs/compbio/veil.htmlAAT http:/genome.cs.mtu.edu/aat.htmlGENEID http:/www.imim.es/GeneIdentification/Geneid/geneid_input.htmlGenlang http:/cbil.humgen.upenn.edu/sdong/genlang_home.htmlGeneParser http:/beagle.colorado.edu/eesnyder/GeneParser.htmlGlimmer http:

26、/www.cs.jhu.edu/labs/compbio/glimmer.htmlMZEF http:/www.cshl.org/genefinderProcrustes http:/www-hto.usc.edu/software/procrustes/Tandem Repeats Finderhttp:/C3.biomath.mssm.edu/trf.htmlRepeatshttp:/bioweb.pasteur.fr/seqanal/interfaces/repeats.html基因分类GO Annotatorhttp:/udgenome.ags.udel.edu/gofigure蛋白质

27、结构预测分析Expasy http:/www.expasy.ch/CBShttp:/www.cbs.dtu.dkPredicting protein secondary structure http:/dot.imgen.bcm.tmc.edu:9331/pssprediction/pssp.htmlPredicting protein 3D Structures http:/dove.embl-heidelberg.de/3D/Predicting protein structures http:/dot.imgen.bcm.tmc.edu:9331/seq-search/struc-pre

28、dict.html其它分析工具和软件BioEdithttp:/www.mbio.ncsu.edu/BioEdit/bioedit.htmlPrimer3（PCR引物设计）http:/frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgiPutative DNA Sequencing Errors Check http:/www.bork.embl-heidelberg.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 http:/dot.imgen.bcm.tmc.edu:9331/seq-util/seq-util.htmlWebcutter Translate DNA to protein http:/www.expasy.ch/tools/dna.htmlABIM http:/www-biol.univ-mrs.fr/english/logligne.htmlsequence motifs:Pfa