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资源共享,常用生物信息学方面网站大全

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发表于 2005-1-5 08:53:34 | 显示全部楼层 |阅读模式
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
 

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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