基因酷 基因库 Genecool » 生物信息学及其应用 » 【转载】常用的生物信息学网址大全
http://www.pdb.org NDBhttp://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 3Dimagehttp://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.html Protein Kinase Resource (PKR) http://www.sdsc.edu/kinases/ LIGAND http://www.genome.ad.jp/dbget/ligand.html WIThttp://www.cme.msu.edu/WIT/ EcoCyc http://ecocyc.PangeaSystems.com/ecocyc/ UM-BBDhttp://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.org GrainGene http://www.graingenes.org Botanical Databases http://www.transgenica.com/botanicaldatabase.htm Botanical Data http://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/fpc http://www.genome.arizona.edu 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 Maize genome http://www.agron.missouri.edu Barley genome http://www.css.orst.edu/Research/barley/nabgmp.htm Forage grasses genomes http://forages.orst.edu/
http://www.forages.css.orst.edu/Topics/Species/Grasses/ Triticum genomes http://wheat.pw.usda.gov/index.shtml Arabidopsis genome http://www.arabidopsis.org SoyBase http://129.186.26.94 Alfalfa genome http://www.alfalfa.ksu.edu Cotton genome http://cottongenomecenter.ucdavis.edu Glycine max genome http://www.zmdb.iastate.edu/PlantGDB/glycine_max.html
http://www.zmdb.iastate.edu/PlantGDB C. elegans genome http://www.acedb.org 藻类(Chlamydomonas)基因组 http://www.biology.duke.edu/chlamy_genome 粘菌(Dictyostelium)基因组 http://dictygenome.bcm.tmc.edu Animal genomes (ArkDB) http://www.thearkdb.org 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/ Rice Genetics Newsletter http://www.gramene.org/newsletters/rice_genetics Proceedings of the National Academy of Sciences USA (PNAS) http://intl.pnas.org 关键词为基础的数据库检索 Entrezhttp://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 Entrezhttp://www.ncbi.nlm.nih.gov/Entrez/batch.html Sequence Retrieval System, India http://bioinfo.ernet.in:80/srs5/ Sequence Retrieval System, Singaporehttp://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 BLASThttp://www.ncbi.nlm.nih.gov/BLAST/ FASTAhttp://www.ebi.ac.uk/fasta33/index.html 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 packagehttp://www.gcg.com/ PHYLIPhttp://evolution.genetics.washington.edu/phylip.html MEGA/METREE http://www.bio.psu.edu/imeg Hennig86 http://www.vims.edu/~mes/hennig/software.html GAMBIThttp://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 ClustalX ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX MEGA http://www.megasoftware.net 基因结构预测分析 GENSCAN http://genes.mit.edu/GENSCAN.html http://bioweb.pasteur.fr/seqanal/interfaces/genscan-simple.html http://bioweb.pasteur.fr 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/ Grailhttp://compbio.ornl.gov/Grail-1.3/ GrailEXP http://grail.lsd.ornl.gov/grailexp/ GeneMarkhttp://opal.biology.gatech.edu/GeneMark/eukhmm.cgi 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 Genlanghttp://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/ 基因分类 GO Annotator http://udgenome.ags.udel.edu/gofigure 蛋白质结构预测分析 Expasyhttp://www.expasy.ch/ CBS http://www.cbs.dtu.dk 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 FastMhttp://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 ABIMhttp://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 PRINTShttp://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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