常用生物信息学数据库和分析工具网址.docx

常用生物信息学数据库和分析工具网址.docx

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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

数据库

因特网网址

网上生物信息学教程

EBI自修课程

http:

//www.ebi.ac.uk/2can

NCBI自修课程

http:

//www.ncbi.nlm.nih.gov/Education

自修课程

http:

//lectures.molgen.mpg.de/online_lectures.html

生物信息学常问的问题

http:

//bioinformatics.org/faq/

生物信息学机构

NCBI

http:

//www.ncbi.nlm.nih.gov/

InternationalNucleotideSequenceDatabaseCollaboration.

http:

//www.ncbi.nlm.nih.gov/collab/

EBI

http:

//www.ebi.ac.uk/

USDA

http:

//www.nal.usda.gov/

SangerCentre

http:

//genomic.sanger.ac.uk/

北京大学生物信息学中心

数据库信息发布及其它

GenBankReleaseNotes

ftp:

//ncbi.nlm.nih.gov/genbank/gbrel.txt

dbESTsummaryreport

http:

//www.ncbi.nlm.nih.gov/dbEST/dbESTsummarv.html

EMBLreleasenotes

http:

//www.genome.ad.jp/dbget-bin/showman?

embl

DDBJreleasenotes

http:

//www.ddbj.nig.ac.jp/ddbjnew/ddbjrelnote.html

Eukaryoticpromoterdatabasereleasenotes

http:

//www.genome.ad.jp/dbget/dbget2.html

SwissProtreleasenotes

http:

//www.genome.ad.jp/dbget-bin/showman?

swissprot

PIRreleasenotes

http:

//www.genome.ad.jp/dbget-bin/showman?

pir

PRFreleasenotes

http:

//www.genome.ad.jp/dbget-bin/showman?

prf

PDBSTRreleasenotes

http:

//www.genome.ad.jp/dbget-bin/showman?

pdbstr

Prositereleasenotes

http:

//www.genome.ad.jp/dbget-bin/showman?

prosite

PDBreleasenotes

http:

//www.genome.ad.jp/dbget-bin/showman?

pdb

KEGGreleasenotes

http:

//www.genome.ad.jp/dbget-bin/showman?

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:

//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/

PlantRgenedatabase

http:

//www.ncgr.org/rgenes

启动子数据库

Eukaryoticpromoterdatabase

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

基因注释数据库

RAP-DB

http:

//rapdb.lab.nig.ac.jp

基因分类数据库

GeneOntology（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:

//pir.georgetown.edu

PRF

http:

//www.kinasenet.org/pkr/Welcome.do

http:

//www.prf.or.jp/

PDBSTR

http:

//www.genome.ad.jp

Prosite

http:

//www.expasy.org/prosite

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-BindingProteinDatabase

http:

//ndbserver.rutgers.edu/NDB/structure-finder/dnabind/index.html

NMRNucleicAcidsDatabase

http:

//ndbserver.rutgers.edu/NDB/structure-finder/nmr/index.html

ProteinPlusDatabase

http:

//ndbserver.rutgers.edu/NDB/structure-finder/protein/index.html

Swiss3Dimage

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/

EnzymeNomenclatureDatabase

http:

//expasy.hcuge.ch/sprot/enzyme.html

ProteinKinaseResource（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.PangeaS

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

BotanicalData

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

欧洲水稻测序（第12染色体）

s.fr

OryGenesDB（水稻插入突变体）

http:

//orygenesdb.cirad.fr

Maizegenome

http:

//www.agron.missouri.edu

Barleygenome

http:

//www.css.orst.edu/Research/barley/nabgmp.htm

Foragegrassesgenomes

http:

//forages.orst.edu/

http:

//www.forages.css.orst.edu/Topics/Species/Grasses/

Triticumgenomes

http:

//wheat.pw.usda.gov/index.shtml

Arabidopsisgenome

http:

//www.arabidopsis.org

SoyBase

http:

//soybase.agron.iastate.edu

Alfalfagenome

http:

//www.alfalfa.ksu.edu

Cottongenome

http:

//cottongenomecenter.ucdavis.edu

Glycinemaxgenome

http:

//www.zmdb.iastate.edu/PlantGDB/glycine_max.html

http:

//www.zmdb.iastate.edu/PlantGDB

C.elegansgenome

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

Animalgenomes（ArkDB）

http:

//www.thearkdb.org

FlyBase

http:

//flybase.bio.indiana.edu/.bin/fbidq.html?

FBgn0003075

MouseGenomeInformatics

http:

//www.informatics.jax.org/bin/query_accession?

id=MGI:

97555

SaccharomycesGenomeDatabase

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

RiceMutantDatabase

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/

RiceGeneticsNewsletter

http:

//www.gramene.org/newsletters/rice_genetics

ProceedingsoftheNationalAcademyofSciencesUSA（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/

EntrezNucleotideSequenceSearch

http:

//www.ncbi.nlm.nih.gov/Entrez/nucleotide.html

EntrezProteinSequenceSearch

http:

//www.ncbi.nlm.nih.gov/Entrez/protein.html

BatchEntrez

http:

//www.ncbi.nlm.nih.gov/Entrez/batch.html

SequenceRetrievalSystem,India

http:

//bioinfo.ernet.in:

80/srs5/

SequenceRetrievalSystem,Singapore

http:

//www.bic.nus.edu.sg:

80/srs5/

SequenceRetrievalSystem,US

http:

//iubio.bio.indiana.edu:

80/srs/srsc

SequenceRetrievalSystem,UK

http:

//srs.ebi.ac.uk/

GetEntryNucleotide&ProteinSequenceSearch

http:

//ftp2.ddbj.nig.ac.jp:

8000/getstart-e.html

DatabaseSearchwithKeyWords

http:

//ftp2.ddbj.nig.ac.jp:

8080/dbsearch-e-new.html

DBGET/LinkDB

http:

//www.genome.ad.jp/dbget/

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/bic_sw/

SSearch

rs.fr/bin/ssearch-guess.cgi

ElectronicPCR

http:

//www.ncbi.nlm.nih.gov/STS/

Proteomeanalysis

http:

//www.ebi.ac.uk/proteome/

Globalalignment

http:

//genome.cs.mtu.edu

多序列分析

Clustalmultiplesequencealignment

http:

//dot.imgen.bcm.tmc.edu

BCM

http:

//dot.imgen.bcm.tmc.edu:

9331/multi-align/multi-align.html

EBIClustalW

http:

//www.ebi.ac.uk/clustaw/index.html

Clustalmultiplesequencealignment

http:

//genome.cs.mtu.edu

修饰对序列对位排列结果的格式（Boxshade）

http:

//www.ch.embnet.org/software/BOX_form.html

系谱分析

PAUP

http:

//onyx.si.edu/PAUP/

EBIClustalWanalysis

http:

//www.ebi.ac.uk

GCGpackage

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

Phylogeneticanalysis

http:

//www.unl.edu/stc-95/ResTools/biotools/biotools2.html

ClustalX

ftp:

//ftp-igbmc.u-strasbg.fr/pub/ClustalX

MEGA

TreeView

http:

//taxonomy.zoology.gla.ac.uk/rod/treeview.html

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:

//www.bioscience.org/urllists/genefind.htm

GeneFinding

GeneFeatureSearches

http:

//dot.imgen.bcm.tmc.edu

Grail

http:

//compbio.ornl.gov/Grail-1.3

GrailEXP

http:

//compbio.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/

TandemRepeatsFinder

http:

//C3.biomath.mssm.edu/trf.html

Repeats

http:

//bioweb.pasteur.fr/seqanal/interfaces/repeats.html

基因分类

GOAnnotator

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

Predictingproteinsecondarystructure

http:

//dot.imgen.bcm.tmc.edu:

9331/pssprediction/pssp.html

Predictingprotein3DStructures

http:

//dove.embl-heidelberg.de/3D/

Predictingproteinstructures

http:

//dot.imgen.bcm.tmc.edu:

9331/seq-search/struc-predict.html

其它分析工具和软件

BioEdit

http:

//www.mbio.ncsu.edu/BioEdit/bioedit.html

Primer3（PCR引物设计）

http:

//frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi

PutativeDNASequencingErrorsCheck

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

WebSignalScan

http:

//www.dna.affrc.go.jp/htdocs/sigscan/signal.html

BCMSearchLauncher

http:

//dot.imgen.bcm.tmc.edu:

9331/seq-util/seq-util.html

Webcutter

TranslateDNAtoprotein

http:

//www.expasy.ch/tools/dna.html

ABIM

http:

//www-biol.univ-mrs.fr/english/logligne.html

sequencemotifs:

Pfa