[Bioc-devel] rGADEM is now available

Droit Arnaud Arnaud.Droit at ircm.qc.ca
Thu Feb 11 18:08:34 CET 2010

Hello everyone,

rGADEM a new package for de novo motif discovery is available on Bioconductor.

We propose an efficient method which combines spaces dyad and an expectation-maximization algorithm (EM).
Candidates words (four to six nucleotide) for constructing spaced dyads are prioritized by their degree of overrepresentation on the input sequence data.
Spaced dyads are converted into starting position weight matrices (PWMs).
rGADEM then employs a genetic algorithm, with an embedded EM to improve starting PWMs, to guide the evolution of a population of spaced dyads towards one whose entropy score  are more statistically significant.

Please, let me know of you have comments, suggestions.


Arnaud Droit, Ph.D
Computational Biology Unit
Institut de Recherches Cliniques de Montréal
arnaud.droit at ircm.qc.ca<mailto:arnaud.droit at ircm.qc.ca>

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