An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20061108/ 3ff77e2a/attachment.pl

For motif discovery in promoter sequences you may want to take a look at the cosmo package (not part of BioC yet?) at: http://www.stat.berkeley.edu/~sandrine/software.html or http://cosmoweb.berkeley.edu/intro.html Thomas On Wed 11/08/06 10:55, Lakshmanan Iyer 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Thomas Girke, Ph.D. 1008 Noel T. Keen Hall Center for Plant Cell Biology (CEPCEB) University of California Riverside, CA 92521

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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >