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")

Vignettes (Documentation)

Package Downloads

cosmo.pdf
Source cosmo_1.6.0.tar.gz
Windows binary cosmo_1.6.0.zip
OS X binary cosmo_1.6.0.tgz

Details

biocViews
Depends R, methods, utils, seqLogo
Suggests cosmoGUI
Imports
SystemRequirements
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
dependsOnMe cosmoGUI
suggestsMe