Dear Arici yes. Best wishes Wolfgang 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > Bioc-sig-sequencing at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Best wishes Wolfgang -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber/contact

Hi Arici yes. For discovering such sequences, look at the "cosmo" package: http://www.bioconductor.org/packages/bioc/vignettes/cosmo/inst/doc/cos mo.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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > Bioc-sig-sequencing at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Best wishes Wolfgang -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber/contact