Hi Everyone
1. I will indeed check out COSMO and post my experience for others on the
list.
2. I think that the mapping of CONFAC data would be very useful to the
community and me of course!
-Thanks
-Lax



On 11/8/06, Oliver Bembom <bembom@gmail.com> wrote:
>
> Hi Lax,
>
> The cosmo package that Thomas is referring to implements an algorithm that
> is
> very similar to MEME except that it also allows the user to impose
> constraints on the position weight matrix of the unknown motif, such as
> "The
> information content in this region of the motif must be greater than
> 1.0", "The GC content in this region of the motif must be greater than
> 75%",
> or "The motif must contain the submotif GCT somewhere within it". Of
> course,
> you can also run the algorithm without any constraints, which is then
> pretty
> much equivalent to MEME.
>
> The package is currently under review by Bioconductor and should be posted
> soon. In the meantime you can get the latest version of the R package at
>
> http://cosmoweb.berkeley.edu/software.html
>
> For more information about the package as well as an implementation in the
> form of a web application, take a look at
>
> http://cosmoweb.berkeley.edu/
>
> Oliver
>
>
> On 11/8/06, Lakshmanan Iyer <laxvid@gmail.com> wrote:
> > Hi Everyone
> >  I am doing a time series microarray expression analysis using
> Bioconductor
> > and it would be great if I could do the promter analysis also from
> within
> > Bioconductor.
> >  Has anyone worked with the TFBS BioPerl module to perfome promoter
> analysis
> > on the promoters of clusters of genes?
> >
> >
> > -Thanks
> > -Lax
> > Research Assistant Professor of Neuroscience
> > Tufts University School of Medicine
> > Boston
> > MA 02111
> >
> >         [[alternative HTML version deleted]]
> >
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> >
>

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