[BioC] matching transcription factor binding sites

[Herve Pages]

Hi Hans,

Hans-Ulrich Klein wrote:
> Dear all,
> 
> I want to locate transcription factor binding sites (tfbs) within a 
> given sequence. The tfbs are derived from databases like transfac or 
> jaspar and are described by matrices. Are there algorithms for locating 
> tfbs matches (e.g. "matinspector") implemented in bioconductor? I could 
> not find one.

I assume that your matrices are Position Weight Matrices? There is no facility
in the Biostrings package for matching PWM to a DNA sequence but that would be
easy to add. In fact, I've already fully described how to implement such facility
in a separate package and on top of Biostrings basic containers (i.e. DNAString
objects) during the lab I gave for the "Advanced R for Bioinformatics" course
back in February this year:

   http://bioconductor.org/workshops/2008

Follow "Advanced R for Bioinformatics" ->  "Interfaces to C (Lab)"

The simpleMatchPWM_0.99.0.tar.gz package contains the matchPWM() function for
finding all matches of a PWM in a given sequence. Unfortunately, the package
was depending on a devel version of Biostrings that has changed since then, and
those changes broke simpleMatchPWM 0.99.0. Let me know if this is what you are
looking for and I'll fix the package (this should be straightforward).

Cheers,
H.

> 
> Regards,
> Hans-Ulrich
> 
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