生物信息学软件
生物信息学软件
2011/11/11 10:15:25
综合
| NCBI | web | http://www.ncbi.nlm.nih.gov |
| EBI | web | http://www.ebi.ac.uk |
| CBI | web | http://www.cbi.pku.edu.cn |
| ExPASy Proteomics tools | web | http://ca.expasy.org/tools/ |
| EMBOSS | web | http://www.ebi.ac.uk/emboss/ |
| - | - | http://211.161.196.209/w2h/ |
| - | local | http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ |
| - | - | http://www.emboss.org/ |
| Web-based Sequence Analysis | web | http://analysis.molbiol.ox.ac.uk/pise_html/index.html |
| BCM Search Launcher | web | http://searchlauncher.bcm.tmc.edu/ |
| - | local | ftp://ftp.hgsc.bcm.tmc.edu/sl/software/search-launcher/ |
| Pasteur Institute | web | http://bioweb.pasteur.fr/intro-uk.html |
| SeWeR | web | http://iubio.bio.indiana.edu/webapps/SeWeR/ |
| The Sequence Manipulation Suite | web | http://www.ualberta.ca/~stothard/javascript/index.html |
| CBS Prediction Servers | web | http://www.cbs.dtu.dk/services/ |
| CMS Molecular Biology Resource | web | http://restools.sdsc.edu/ |
Alignment
| ClustalW | web | http://www.ebi.ac.uk/cgi-bin/newclustalw.pl |
| DCA | web | http://bibiserv.techfak.uni-bielefeld.de/dca/ |
| SIM4 | web | http://biom3.univ-lyon1.fr/sim4.html |
| SIM | web | http://ca.expasy.org/tools/sim-prot.html |
| DIALIGN | web | http://bibiserv.techfak.uni-bielefeld.de/cgi-bin/dialign_submit |
Pairwise alignment
| bl2seq | web | http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html |
| align | web | http://www.ebi.ac.uk/emboss/align/ |
Sequence Viewers and editor
| GeneDoc | local | http://www.psc.edu/biomed/genedoc/ |
| CHROMA | local | http://www.lg.ndirect.co.uk/chroma/ |
| BioEdit | local | http://www.mbio.ncsu.edu/BioEdit/bioedit.html |
Sequence format conversion tools
| READSEQ | web | http://bimas.dcrt.nih.gov/molbio/readseq/ |
| Reverse Complement | web | https://www.bioinformatics.org/sms/rev_comp.html |
| Reverse Complement | web | http://www.ualberta.ca/~stothard/javascript/rev_comp.html |
| RevComp | local | http://www.cmrsinc.com/sequence/RevComp.exe |
Translation tool
| Transeq | web | http://www.ebi.ac.uk/emboss/transeq/index.html |
| Translate | web | http://us.expasy.org/tools/dna.html |
| Translation Machine | web | http://www2.ebi.ac.uk/translate/ |
| DNA Sequence Translator | web | http://biocommons.bcc.washington.edu/services/psoftware/dnatranslator/index.html |
Sequence search
| BLAST | web | http://www.ncbi.nlm.nih.gov/BLAST/ |
| - | local | NCBI－Blast ftp://ftp.ncbi.nlm.nih.gov/blast/ WU-Blast http://blast.wustl.edu/ |
| Fasta | web | http://www.ebi.ac.uk/fasta33/index.html |
| MPsrch | web | http://www.ebi.ac.uk/MPsrch/index.html |
| Smith-Waterman Reverse-Frame Search | web | http://www.dna.affrc.go.jp/htbin/tswn.pl |
| ESTblast | web | http://www.hgmp.mrc.ac.uk/ESTBlast/ |
Sequence search by Genome
| NCBI:Genomic BLAST pages | web | http://www.ncbi.nlm.nih.gov/BLAST/ |
| GOLD | web | http://wit.integratedgenomics.com/GOLD/ |
UTR analysis
| UTRhome | - | http://bighost.area.ba.cnr.it/BIG/UTRHome/ |
Signal Scan
| SignalP | web | http://www.cbs.dtu.dk/services/SignalP-2.0/ |
| - | - | http://bimas.dcrt.nih.gov/molbio/signal/ |
| - | - | http://www.dna.affrc.go.jp/htdocs/sigscan/signal.html |
| - | local | Send inquiries by e-mail to software@cbs.dtu.dk |
| TargetP | web | http://www.cbs.dtu.dk/services/TargetP/ |
| SIGSCAN | web | http://bimas.dcrt.nih.gov/molbio/signal/ |
| ChloroP | web | http://www.cbs.dtu.dk/services/ChloroP/ |
| NetPhos | web | http://www.cbs.dtu.dk/services/NetPhos/ |
Promoter Scan
| PROSCAN | web | http://bimas.dcrt.nih.gov/molbio/proscan/ |
| TRANSFAC | web | http://transfac.gbf.de/TRANSFAC/ |
| COMPEL | web | http://compel.bionet.nsc.ru/compel/compel.html |
| - | local | http://compel.bionet.nsc.ru/cgi-bin/download/download.pl |
| Promoter 2.0 | web | http://www.cbs.dtu.dk/services/Promoter/ |
| PROMOTER SCAN II | web | http://www.molbiol.ox.ac.uk/promoterscan.htm |
| Promoter Prodiction | web | http://www.fruitfly.org/seq_tools/promoter.html |
Protein Motif&Domain analysis
| InterProScan | web | http://www.ebi.ac.uk/interpro/scan.html |
| - | local | ftp://ftp.ebi.ac.uk/pub/databases/interpro/ |
| SMART | web | http://smart.embl-heidelberg.de/ |
| PROSITE | web | http://us.expasy.org/prosite/ |
| - | local | http://us.expasy.org/ftp/databases/prosite/ |
| Pfam | web | http://pfam.wustl.edu/ |
| - | local | ftp://ftp.genetics.wustl.edu/pub/Pfam/ |
| CDD | web | http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml |
| PRINTS | web | http://bioinf.man.ac.uk/dbbrowser/PRINTS/ |
| ProDom | web | http://prodes.toulouse.inra.fr/prodom/2002.1/html/home.php |
| ELM | web | http://elm.eu.org/ |
| TIGRFAMs | web | http://www.tigr.org/TIGRFAMs/ |
| - | local | ftp://ftp.tigr.org/pub/data/TIGRFAMs |
Transmembrane Domains
| TMHMM | web | http://www.cbs.dtu.dk/services/TMHMM-2.0/ |
| PRED-TMR | web | http://o2.db.uoa.gr/PRED-TMR/ |
| DAS | web | http://www.sbc.su.se/~miklos/DAS/ |
| TopPred | web | http://www.sbc.su.se/~erikw/toppred2/ |
| TMpred | web | http://www.ch.embnet.org/software/TMPRED_form.html |
Post-translational modifications
| YinOYang | web | http://www.cbs.dtu.dk/services/YinOYang/ |
| GlycoMod | web | http://ca.expasy.org/tools/glycomod/ |
| FindMod | web | http://ca.expasy.org/tools/findmod/ |
| PhosphoBase | web | http://www.cbs.dtu.dk/databases/PhosphoBase/ |
| O-GlycBase | web | http://www.cbs.dtu.dk/databases/OGLYCBASE/ |
| NetOGlyc | web | http://www.cbs.dtu.dk/services/NetOGlyc/ |
| NetPhos | web | http://www.cbs.dtu.dk/services/NetPhos/ |