cosmo

Supervised detection of conserved motifs in DNA sequences

Bioconductor version: 2.8

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 <oliver.bembom at gmail.com>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("cosmo")

Documentation

PDF R Script Supervised detection of conserved motifs in DNA sequences with cosmo
PDF   Reference Manual

Details

biocViews SequenceMatching
Depends R (>= 2.4.0), methods, utils, seqLogo
Imports
Suggests cosmoGUI
System Requirements
License file LICENSE
URL http://cosmoweb.berkeley.edu/intro.html, http://www.bepress.com/sagmb/vol6/iss1/art8
Depends On Me cosmoGUI
Imports Me
Suggests Me mosaics
Version 1.18.0
Since Bioconductor 2.0 (R-2.5)

Package Downloads

Package Source cosmo_1.18.0.tar.gz
Windows Binary cosmo_1.18.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary cosmo_1.18.0.tgz
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