Hi Kasper, matchPWM is great and really fast.
I will have to think how to estimate the FDR as this motif search reports many hits. Thank you, Ivan Ivan Gregoretti, PhD National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health 5 Memorial Dr, Building 5, Room 205. Bethesda, MD 20892. USA. Phone: 1-301-496-1016 and 1-301-496-1592 Fax: 1-301-496-9878 On Tue, Jan 25, 2011 at 10:52 AM, Kasper Daniel Hansen <[email protected]> wrote: > > I would start with > Biostrings::matchPWM > The function name sounds promising :) > > Kasper > > On Tue, Jan 25, 2011 at 10:36 AM, Ivan Gregoretti <[email protected]> wrote: > > Hello everybody, > > > > Introduction: > > I have a Position Weigh Matrix that characterises the binding DNA > > sequence of a novel transcription factor. > > > > Goal: > > I want to find the genomic positions that are good matches for my PWM. > > > > Question: > > What are my options among the Bioconductor packages? > > > > Thank you, > > > > Ivan > > > > > > Ivan Gregoretti, PhD > > National Institute of Diabetes and Digestive and Kidney Diseases > > National Institutes of Health > > 5 Memorial Dr, Building 5, Room 205. > > Bethesda, MD 20892. USA. > > Phone: 1-301-496-1016 and 1-301-496-1592 > > Fax: 1-301-496-9878 > > > > _______________________________________________ > > Bioc-sig-sequencing mailing list > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
