cosmo

Supervised detection of conserved motifs in DNA sequences

cosmo searches a set of unaligned DNA sequences for a shared motif that may, for example, represent a common transcription factor binding site. The algorithm is similar to MEME, but also allows the user to specify a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may include bounds on the information content across certain regions of the unknown motif, for example, and can often be formulated on the basis of prior knowledge about the structure of the transcription factor in question. The unknown motif width, the distribution of motif occurrences (OOPS, ZOOPS, or TCM), as well as the appropriate constraint set can be selected data-adaptively.

Author Oliver Bembom, Fabian Gallusser, and Sandrine Dudoit
Maintainer Oliver Bembom

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("cosmo")

Documentation

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Supervised detection of conserved motifs in DNA sequences with cosmo
Reference Manual
Package source cosmo_1.8.0.tar.gz
Windows binary cosmo_1.8.0.zip
MacOS X 10.4 (Tiger) binary cosmo_1.8.0.tgz
MacOS X 10.5 (Leopard) binary cosmo_1.8.0.tgz
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Details

biocViews
Depends
R , methods , utils , seqLogo
Imports
Suggests
System Requirements
License Free for research purposes only. For details, see COPYING or type license.cosmo() in R.
URL http://cosmoweb.berkeley.edu/intro.html, http://www.bepress.com/sagmb/vol6/iss1/art8
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