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://www.ncbi.nlm.nih.gov/dbGSS/index.html Genome (NCBI) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Geno me 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.htmlPromoter Prediction Website

http://bip.weizmann.ac.il/toolbox/seq_analysis/promoters.html#databases
http://www.fruitfly.org/seq_tools/promoter.html
http://sdmc.lit.org.sg/promoter/CGrich1_0/CGRICH.htm
http://www.gene-regulation.com/pub/programs.html#pmatch
http://ihome.cuhk.edu.hk/~b400559/arraysoft_pathway.html#Promoter
http://www.dna.affrc.go.jp/PLACE/signalup.html
http://intra.psb.ugent.be:8080/PlantCARE/
http://www.cbs.dtu.dk/services/Promoter/
http://bimas.dcrt.nih.gov/molbio/proscan/
http://thr.cit.nih.gov/molbio/signal/

转录因子数据库

Plant Transcription Factor Database

http://planttfdb.cbi.pku.edu.cn/

Animal Transcription factor database

http://www.bioguo.org/AnimalTFDB/

The JASPAR database

http://jaspar.genereg.net/

PAZAR: Search for Transcription Factors (TFs)

http://www.pazar.info/

Rice TF Database

http://ricephylogenomics.ucdavis.edu/tf/

Promoter Database

https://cb.utdallas.edu/cgi-bin/TRED/tred.cgi?process=home

FRANSFAC http://transfac.gbf.de ooTFD http://www.ifti.org共表达数据库

植物 ATTED-II 

http://atted.jp/

水稻RiceFREND

http://ricefrend.dna.affrc.go.jp/

动物 COXPRESdb

http://coxpresdb.jp/

基因分类数据库Gene Ontology (GO) http://www.geneontology.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-todayProsite 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/dna bind/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/prot ein/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/ 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 

综合数据库

Phytozome:http://www.phytozome.net/

Ensemble:http://ensembl.gramene.org/genome_browser/index.html 

NCBI：http://www.ncbi.nlm.nih.gov/assembly/?term=

基因组复制数据库PGDD

http://chibba.agtec.uga.edu/duplication/

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.ht ml 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?FBgn0003 075 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/Sacch DB?find+Locus+%22PGK1%22 多种基因组数据库 http://www.hgmp.mrc.ac.uk/GenomeWeb文献数据库

几乎所有SCI文献免费下载网站

http://www.sci-hub.cc/

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://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://searchlauncher.bcm.tmc.edu/multi-align/multi-ali gn.html BCM http://searchlauncher.bcm.tmc.edu/ 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/Resea rch/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

AUGUSTUS

http://bioinf.uni-greifswald.de/webaugustus/

Genewise

http://www.ebi.ac.uk/Tools/psa/genewise/

GENSCAN http://genes.mit.edu/GENSCAN.html http://bioweb.pasteur.fr/seqanal/interfaces/genscan-si mple.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/ Grail http://compbio.ornl.gov/Grail-1.3/ GrailEXP http://grail.lsd.ornl.gov/grailexp/ GeneMark http://opal.biology.gatech.edu/GeneMark/eukhmm.cgi http://genemark.biology.gatech.edu/GeneMark/hmmcho ice.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_i nput.html Genlang http://cbil.humgen.upenn.edu/~sdong/genlang_home.ht ml 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Expasy http://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-p redict.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.ht ml 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_i nfo.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 

欢迎大家补充其他有用的网站！

参考来源：http://wenku.baidu.com/link?url=DVEjdUp4V749cIpUHWyo-v8vmy6azNp0d_XqmPFSo7q6h8Mk30n6wqnsAChgBImuiaKECuN0jXPTZSqD8_z5nDtLwNajfCqiwd2a5QJwgOy