Consensus from Multiple Alignments

[Anders Gorm Pedersen]

Tim Spahlinger wrote:

> Can somebody recommend a web site (preferred) or a software
> package (I'd rather save my limited funding) that will give
> me a consensus sequence of bases derived from the multiple
> alignments of several sequences? 

[...]

Call me a puritan, but I would warn against using consensus sequences for most
purposes (most of the information contained in the alignment is thrown away, a
consensus sequence is not necessarily represented even once in the original data
set, etc., etc.). 

A very informative alternative is a sequence logo. An online server is available
at:

  http://www.bio.cam.ac.uk/cgi-bin/seqlogo/logo.cgi

More info on logos:

  http://www-lmmb.ncifcrf.gov/~toms/index.html#Sequence.Logos

More info on information theory:

  http://www-lecb.ncifcrf.gov/~toms/paper/trieste1996/

Best regards,
Anders Gorm Pedersen


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 Anders Gorm Pedersen, cand.scient., Ph.D.  (gorm at cbs.dtu.dk)

 Center for Biological Sequence Analysis
 Technical University of Denmark
 Bldg 208, DK-2800 Lyngby, Denmark

 phone: (+45) 45 25 24 84
 fax:   (+45) 45 93 15 85

 Web: http://www.cbs.dtu.dk/gorm/
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