GenBank（美国）

http://www.ncbi.nlm.nih.gov/

ENA（欧洲）

http://www.ebi.ac.uk/

DDBJ（日本）

http://www.ddbj.nig.ac.jp/

 

1. 核苷酸数据库

NAR

http://www.oxfordjournals.org/nar/database/c/

dbEST (Database of Expressed Sequence Tags)

http://www.ncbi.nlm.nih.gov/dbEST/index.html

UniGene

       http://www.ncbi.nlm.nih.gov/unigene/statistics/

TSA

http://www.ncbi.nlm.nih.gov/genbank/tpa

dbSTS (Database of Sequence Tagged Sites)

http://www.ncbi.nlm.nih.gov/dbSTS/index.html

dbGSS (Database of Genome Survey Sequences)

http://www.ncbi.nlm.nih.gov/dbGSS/index.html

HTGS (High-Throughput Genomic Sequences)

http://www.ncbi.nlm.nih.gov/HTGS/

Genome

http://www.ncbi.nlm.nih.gov/genome

http://asia.ensembl.org/info/about/species.html

http://genomesonline.org/cgi-bin/GOLD/index.cgi

dbSNP (Database of Single Nucleotide Polymorphisms)    

http://www.ncbi.nlm.nih.gov/snp

dbVar (Database of  Genomic Structural Variation)   

http://www.ncbi.nlm.nih.gov/dbvar

EPD (Eukaryotic Promoter Database)

http://www.epd.isb-sib.ch/

PlantProm (plant promoter database)

miRBase         
    http://www.mirbase.org/

 

 

2. 蛋白质数据库

UniProt
    http://www.uniprot.org/

PIR (Protein Information Resource)

http://pir.georgetown.edu

PRF (Protein Research Foundation)

http://www.prf.or.jp/

PDBSTR (Re-Organized Protein Data Bank)

http://www.genome.jp/dbget-bin/www_bfind?pdbstr

Prosite

       http://www.expasy.org/prosite

 

 

3. 结构数据库

PDB (Protein Data Bank)

    http://www.rcsb.org

NDB (Nucleic Acid Database)

http://ndbserver.rutgers.edu

PDIdb (Protein-DNA Interface Database)

http://melolab.org/pdidb

Conserved Domain Search

http://www.ncbi.nlm.nih.gov/Structure/cdd/docs/cdd_search.html

RNAfold WebServer

http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi

 

 

4. 酶和代谢数据库

KEGG (Kyoto Encyclopedia of Genes and Genomes)

http://www.genome.ad.jp/kegg/

PKR (Protein Kinase Resource)

http://pkr.genomics.purdue.edu/pkr/

 

 

5. 物种分类数据库

Taxonomy数据库

http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html

 

 

6. 文献数据库

PubMed

http://www.ncbi.nlm.nih.gov/PubMed/

OMIM (Online Mendelian Inheritance in Man)

http://www.ncbi.nlm.nih.gov/omim

Agricola

http://agricola.nal.usda.gov/

eTBLAST

http://etest.vbi.vt.edu/etblast3/

 

 

7. 序列比对

BLAST (Basic Local Alignment Search Tool)

http://blast.ncbi.nlm.nih.gov/

Constraint-based Multiple Alignment Tool

http://www.ncbi.nlm.nih.gov/tools/cobalt/

FASTA 检索

http://www.ebi.ac.uk/Tools/sss/

EBI的ClustalW

http://www.ebi.ac.uk/Tools/msa/clustalw2/

Boxshade

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

ESPript

http://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi

GeneDoc

http://www.nrbsc.org/gfx/genedoc

 

 

8. 系统发生分析

MEGA

 

 

9. 设计引物

Primer-BLAST

http://www.ncbi.nlm.nih.gov/tools/primer-blast/

Primer3

http://frodo.wi.mit.edu/primer3

http://redb.ncpgr.cn/modules/redbtools/primer3.php

 

 

10. 酶切位点

NEBcutter

http://tools.neb.com/NEBcutter2/index.php

EnzymeX

http://www.mekentosj.com/science/enzymex

RestrictionMapper

http://www.restrictionmapper.org/

DNAMAN

    http://www.lynnon.com/pc/pcmain_new.html

 

 

11. 基因预测和基因结构分析 要确认核苷酸数是否一致

Repeatmasker

http://www.repeatmasker.org/

ORF finder(原核生物或mRNA序列)

http://www.ncbi.nlm.nih.gov/projects/gorf/

 

GeneWise

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

CDS:

Softberry(Eukaryota, Bacteria, Viruses)  好一些 正负链

http://linux1.softberry.com/berry.phtml

G - predicted gene number, starting from start of sequence; 
       Str - DNA strand (+ for direct or - for complementary); 
       Feature - type of coding sequence: CDSf - First (Starting with Start codon), CDSi - internal    (internal exon), CDSl - last coding segment, ending with stop codon); 
       TSS - Position of transcription start (TATA-box position and score); 
       Start and End - Position of the Feature; 
       Weight - Log likelihood*10 score for the feature; 
       ORF - start/end positions where the first complete codon starts and the last codon ends.

GenScan(Vertebrate, Arabidopsis, Maize)

http://genes.mit.edu/GENSCAN.html

AUGUSTUS(真核基因)

http://augustus.gobics.de/

GeneMark(真核、原核和病毒)

http://exon.biology.gatech.edu/

N-SCAN/Twinscan

http://mblab.wustl.edu/nscan/

NNPP分析转录起始位点

http://www.fruitfly.org/seq_tools/promoter.html

Promoter 2.0 Prediction Server寻找启动子

http://www.cbs.dtu.dk/services/Promoter/

PROSCAN寻找转录因子结合位点

http://www-bimas.cit.nih.gov/molbio/proscan/

PLACE (A Database of Plant Cis-acting Regulatory DNA Element)   http://www.dna.affrc.go.jp/PLACE/index.html

非编码RNA基因预测

https://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software

miRNA靶基因预测：

www.mirbase.org/

 

主要预测动物miRNA靶基因  http://www.mirbase.org/search.shtml

miRDB：   http://mirdb.org/miRDB/mining.html   

miRecords：http://mirecords.umn.edu/miRecords/   

 

只能预测细菌sRNA靶基因

TargetRNA2：http://cs.wellesley.edu/~btjaden/TargetRNA2/ 

 

主要用于预测植物miRNA靶基因

WMD3：http://wmd3.weigelworld.org/cgi-bin/webapp.cgi  

 

12. 蛋白质性质和结构分析

ExPASy (Expert Protein Analysis System)

http://www.expasy.org

CBS (Center for Biological Sequence Analysis)

http://www.cbs.dtu.dk/services/

分析蛋白质的pI、Mw、氨基酸组成

http://web.expasy.org/protparam/

分析蛋白质的疏水性

http://web.expasy.org/protscale/

分析蛋白质的保守结构域

http://prosite.expasy.org

http://pfam.sanger.ac.uk/

http://pfam.xfam.org/

NCBI Conserved Domains：http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

SMART：http://smart.embl-heidelberg.de/smart/set_mode.cgi?NORMAL=1

PredictProtein：https://www.predictprotein.org/

预测蛋白质的－螺旋、－折叠及其它二级结构

SOPMA: http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html

PSIPRED http://bioinf.cs.ucl.ac.uk/psipred/

YASPIN http://www.ibi.vu.nl/programs/yaspinwww/

PredictProtein http://ppopen.informatik.tu-muenchen.de

分析蛋白质的三级结构

Phyre2 http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index

SWISS-MODEL Workspace http://swissmodel.expasy.org/workspace/

分析膜蛋白质

SOSUI(预测膜整合蛋白的跨膜区)

http://harrier.nagahama-i-bio.ac.jp/sosui/

DAS(分析原核生物蛋白质的跨膜结构)

 http://www.sbc.su.se/~miklos/DAS/maindas.html

TMpred(分析蛋白质的跨膜结构和在膜上的方向)               http://www.ch.embnet.org/software/TMPRED_form.html

HMMTOP: 分析蛋白质跨膜结构和方向

http://www.enzim.hu/hmmtop/html/submit.html

TopPred: 分析细胞膜蛋白拓扑结构

http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::toppred

TMHMM: 分析蛋白质跨膜结构

http://www.cbs.dtu.dk/services/TMHMM/

big-PI Predictor:分析膜锚定蛋白的GPI位点

http://mendel.imp.ac.at/gpi/gpi_server.html

http://mendel.imp.ac.at/gpi/plant_server.html

http://mendel.imp.ac.at/gpi/fungi_server.html

分析信号肽及其剪切位点

SignalIP

http://www.cbs.dtu.dk/services/SignalP/

Signal-3L: A 3-layer approach for predicting signal peptides

http://www.csbio.sjtu.edu.cn/bioinf/Signal-3L/

PrediSi: PREDIction of SIgnal peptides

http://www.predisi.de/

Phobius: A combined transmembrane topology and signal peptide predictor

http://phobius.sbc.su.se/

PEPLip: Predictor of Signal Peptide and Lipoprotein Cleavage Sites in Proteins

http://gpcr.biocomp.unibo.it/cgi/predictors/spep/pred_spepcgi.cgi

Prediction of importin α-dependent nuclear localization signals

http://nls-mapper.iab.keio.ac.jp/cgi-bin/NLS_Mapper_form.cgi

NucPred  - Predicting Nuclear Localization of Proteins

http://www.sbc.su.se/~maccallr/nucpred/

分析糖链连接点

O－连接糖链的连接位点 http://www.cbs.dtu.dk/services/NetOGlyc

N－连接糖链的连接位点 http://www.cbs.dtu.dk/services/NetNGlyc

分析蛋白质的亚细胞定位

PSORT

http://psort.hgc.jp/

http://www.genscript.com/psort/wolf_psort.html

CELLO：

http://cello.life.nctu.edu.tw/

Subnuclear Compartments Prediction System：     

http://array.bioengr.uic.edu/subnuclear.htm

Proteome Analyst Specialized Subcellular Localization Server：     

http://webdocs.cs.ualberta.ca/~bioinfo/PA/Sub/

Lokero/TargetLoc/SherLoc2/MultiLoc2/YLoc：     

http://abi.inf.uni-tuebingen.de/Research/Systems%20Biology/protein-subcellular-localization

分析化学因子作用蛋白质的位点

PeptideCutter http://web.expasy.org/peptide_cutter/

 

 

 

13. 农业类及物种专属数据库

Gramene：植物比较基因组数据库

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

代谢路径及代谢路径

http://pathway.gramene.org/

动物基因组比较

http://www.ensembl.org

 

14. 综合表达谱数据库

GEO http://www.ncbi.nlm.nih.gov/geo/   GO分析http://bioinfo.cau.edu.cn/agriGO/analysis.php

ATLAS http://www.ebi.ac.uk/gxa/

PLEXdb http://www.plexdb.org/