[Bioc-sig-seq] finding matches to a motif

Ivan Gregoretti ivangreg at gmail.com
Tue Jan 25 23:25:11 CET 2011


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
<kasperdanielhansen at gmail.com> wrote:
>
> I would start with
>  Biostrings::matchPWM
> The function name sounds promising :)
>
> Kasper
>
> On Tue, Jan 25, 2011 at 10:36 AM, Ivan Gregoretti <ivangreg at gmail.com> 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
> > Bioc-sig-sequencing at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >



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