[BioC] http://mail.google.com/mail/?ik=c8b0ad881f&view=cm&fs=1&tf=1&to=Bioconductor%40stat.math.ethz.ch&zx=x780aw-ixfpz3TFBS and Biconductor

[Oliver Bembom]

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 at 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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