常用生物信息学数据库和分析工具网址 常用的数据库工具

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
NCBI

http://www.ncbi.nlm.nih.gov/
International Nucleotide Sequence DatabaseCollaboration.
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.bio.unizh.ch/db/docu.html?data=emrel

Eukaryotic promoter database releasenotes

http://www.genome.ad.jp/dbget/dbget2.html
KEGG release notes
http://www.genome.jp/kegg/docs/relnote.html

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=Genome
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/
启动子数据库Eukaryotic promoter database

http://www.epd.isb-sib.ch/
转录因子数据库FRANSFAC

http://www.gene-regulation.com/pub/databases.html

TFD

http://www.ifti.org
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

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/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 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/PlantGDBC. 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/
Mouse Genome Informatics

http://www.informatics.jax.org/

Saccharomyces GenomeDatabase
http://www.yeastgenome.org/

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 Academyof 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 SequenceSearch
http://www.ncbi.nlm.nih.gov/Entrez/nucleotide.html
Entrez Protein SequenceSearch
http://www.ncbi.nlm.nih.gov/Entrez/protein.html

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 KeyWords

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 sequencealignment
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/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/
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/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/

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 secondarystructure
http://dot.imgen.bcm.tmc.edu:9331/pssprediction/pssp.html
Predicting protein 3DStructures

http://dove.embl-heidelberg.de/3D/
Predicting proteinstructures
http://dot.imgen.bcm.tmc.edu:9331/seq-search/struc-predict.html
其它分析工具和软件
Putative DNA Sequencing ErrorsCheck

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 sequenceanalysis
http://www.bork.embl-heidelberg.de/
功能基因组分析Transcription profilingtechnologies
http://www.ncbi.nlm.nih.gov/ncicgap/expression_tech_info.html
Protocols for cDNA arraytechnology
http://cmgm.stanford.edu/pbrown/array.html
Data management and analysis of geneexpression arrays
http://www.nhgri.nih.gov/DIR/LCG/15k/HTML/
Examples of commercially availablefilter arrays:
GeneFiltersTM (Research Genetics)
http://www.resgen.com
Gene Discovery Arrays (GenomeSystems)
http://www.genomesystems.com
AtlasTM Arrays(CLONTECH)
http://www.clontech.com