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小木虫论坛-学术科研互动平台 » 生物医药区 » 生物科学 » 常用生物信息学数据库和分析工具网址
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[交流] 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

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 ... /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 ... /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/c ... nd+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/mcdb ... /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
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