Consensus from Multiple Alignments

[Tim Spahlinger]

Thank you for your references.  Actually, I agree with your
"puritan" approach and I will try working with this new (to
me) software!

Anders Gorm Pedersen wrote:
> 
> 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
> 
> ---------------------------------------------------------------
>  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/
> ---------------------------------------------------------------