[BioC] motif searching with variable length gaps

[Oliver Bembom]

Hi Heather,

Unfortunately, the cosmo package doesn't have a functionality for this
kind of a search. It is always assumed that the shared motif is of the
same length.

Oliver

On Nov 1, 2007 8:40 AM, Houseman, Heather <Heather.Houseman at vai.org> wrote:
> Dear Bioconductor mailing list:
>
> I've been using cosmo to look for motifs.  I'd like to search for motifs that have a variable length of gaps in the middle. If I specify a range of motif widths with the cosmo function, it uses the width with the lowest BIC value and searches for motifs of only that width.  My dilemma is that the motifs I'm looking for are of variable width.
>
> Thanks in advance for any help!
>
> Heather
>
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