Package: cosmo
Title: Supervised detection of conserved motifs in DNA sequences
Version: 1.20.0
Author: Oliver Bembom, Fabian Gallusser, and Sandrine Dudoit
Description: 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.
Maintainer: Oliver Bembom <oliver.bembom@gmail.com>
Depends: R (>= 2.4.0), methods, utils, seqLogo
Suggests: cosmoGUI
Collate: AllClasses.R AllGenerics.R cosmo.R rseq.R constraints.R zzz.R
License: file LICENSE
URL: http://cosmoweb.berkeley.edu/intro.html,
        http://www.bepress.com/sagmb/vol6/iss1/art8
LazyLoad: yes
biocViews: SequenceMatching
Packaged: 2011-11-01 07:49:46 UTC; biocbuild
Built: R 2.14.0; i386-pc-mingw32; 2011-11-01 12:18:13 UTC; windows
Archs: i386, x64
