Hi BioC developers,

I have submitted a package to Bioconductor that 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 quite 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.

Some simulation studies suggest that cosmo can achieve 2-3 fold greater
sensitivity than MEME even if the user doesn't supply any constraints. If
correct constraints are given, the same simulation studies suggest
sensitivity improvements in the range of 3-3.5 fold.

The source package can be installed from the repository
http://bioconductor.org/packages/2.0/bioc/
; a Windows binary can be found at
http://cosmoweb.berkeley.edu/software.html.

The package cosmoGUI is an add-on to cosmo that allows the user to construct
constraint sets with the help of an interactive GUI. Both cosmo and cosmoGUI
depend on the seqLogo package for plotting sequence logos. cosmoGUI and
seqLogo are available from the same sources as the cosmo package.

The algorithm has also been implemented in the form of a web application
(similar to MEME) that can be accessed at http://cosmoweb.berkeley.edu.

More information is available at http://cosmoweb.berkeley.edu/intro.html as
well as in the paper http://www.bepress.com/sagmb/vol6/iss1/art8.

Any feedback and comments are more than welcome.

Best,

Oliver

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