Package: cosmo
Title: Supervised detection of conserved motifs in DNA sequences
Version: 1.2.0
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 <bembom@berkeley.edu>
Depends: R (>= 2.4.0), methods, utils, seqLogo
Suggests: cosmoGUI
Collate: AllClasses.R AllGenerics.R cosmo.R rseq.R constraints.R zzz.R
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
LazyLoad: yes
biocViews: SequenceMatching
Packaged: Wed Apr 25 04:03:05 2007; biocbuild
Built: R 2.5.0; i386-pc-mingw32; 2007-04-25 06:46:19; windows
