cosmo

Supervised detection of conserved motifs in DNA sequences

Bioconductor version: Development (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

To install this package, start R and enter:

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

Documentation

PDF

R Script

Supervised detection of conserved motifs in DNA sequences with cosmo

Reference Manual

Details

biocViews	SequenceMatching
Depends	R, 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	1.17.0

Package Downloads

Package Source	cosmo_1.17.0.tar.gz
Windows Binary	cosmo_1.17.0.zip (32-bit only)
MacOS 10.5 (Leopard) binary	cosmo_1.17.0.tgz
Package Downloads Report	Download Stats