[BioC] motif searching with variable length gaps

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Hi Heather,

Can you please give some examples of your motifs?

Also showing us the code that you use with cosmo can be useful.

Even if the matchPattern() function in Biostrings doesn't let you control the number
of gaps, there might be workarounds, it all depends what your motifs really look
like. And we need use cases anyway so we know where to put our efforts. Thanks!

H.


Houseman, Heather 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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