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Home > Extras > Bioinformatics For Dummies® Bonus Material
Bioinformatics For Dummies® Bonus Material
By: Jean-Michel Claverie Ph.D., Cedric Notredame Ph.D.
 

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Chapter 9: Building a Multiple Sequence Alignment

Chapter 9 images

BLAST servers integrating multiple alignment methods

URL What You Can Do There
www.expasy.ch/cgi-bin/BLASTEMBnet-CH.pl Extract entire sequences;
Export sequences in FASTA;
Submit sequences to ClustalW;
Submit sequences to Tcoffee
npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_blast.html Extract entire sequences;
Extract sequence fragments;
Export sequences in FASTA;
Submit sequences to ClustalW
srs.ebi.ac.uk Submit sequences to ClustalW

A few ClustalW servers

Name Location URL
EBI Europe www.ebi.ac.uk/clustalw/index.html
EMBnet Europe www.ch.embnet.org/software/ClustalW.html
PIR USA pir.georgetown.edu/pirwww/search/multaln.html
BCM USA searchlauncher.bcm.tmc.edu/multi-align/multi-align.html
GenomeNet Japan clustalw.genome.ad.jp
DDBJ Japan www.ddbj.nig.ac.jp/E-mail/clustalw-e.html
Strasbourg Europe ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/

Other multiple sequence alignment resources over the Internet

Method URL
Tcoffee igs-server.cnrs-mrs.fr/Tcoffee/
www.ch.embnet.org/software/TCoffee.html
www.cmbi.kun.nl/bioinf/tools/T_COFFEE/
Dialign bibiserv.techfak.uni-bielefeld.de/
bioweb.pasteur.fr/seqanal/interfaces/dialign2-simple.html
DCA bibiserv.techfak.uni-bielefeld.de/cgi-bin/dca_submit

Motif-finding methods available online

Method URL
Gibbs Sampler bioweb.pasteur.fr/seqanal/interfaces/gibbs-simple.html
bayesweb.wadsworth.org/gibbs/gibbs.html
Pratt www.ebi.ac.uk/pratt/index.html
eMotif dna.stanford.edu/emotif/
MEME meme.sdsc.edu/meme/website/
TEIRESIAS cbcsrv.watson.ibm.com/Tspd.html
Bioprospector bioprospector.stanford.edu
Improbizer www.soe.ucsc.edu/~kent/improbizer/improbizer.html
BLOCK-Maker blocks.fhcrc.org/blocks/blockmkr/make_blocks.html