[Bioc-sig-seq] finding consensus sites in a set of DNA sequences

[Wolfgang Huber]

Hi Arici

yes. For discovering such sequences, look at the "cosmo" package: 
http://www.bioconductor.org/packages/bioc/vignettes/cosmo/inst/doc/cosmo.pdf

For simply identifying known candidate sequences, 
vMatchPattern/vcountPattern in "Biostrings" (which also offers 
components with which you can build tools to try your own ideas).

Arici Pogonici scripsit 12/05/2009 11:28 PM:
> Hi dear group -
> 
> please could you let me know whether there is any command in R/BioC that
> would allow to identify long consensus sites (16-20 nt length) in a set of
> DNA sequences.
> 
> Thanks a lot !
> 
> Arici
> 
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-- 

Best wishes
      Wolfgang


--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber/contact