Dear all,


rGADEM is a de novo motif discovery tool for large scale genomic data that
is part of an integrated pipeline for ChIP-seq analysis (PICS/rGADEM/MotIV)
[1]. The program uses openMP in order to greatly reduce some parts of the
calculation.


We are proud to announce a new version of the software, rGADEM 2.0. The code
is now up-to-date with the latest changes in the GADEM, the c version of the
program.


Notably, two new parameters have been introduced: nmotifs and maskR. With
nmotifs, it is now possible to stop the analysis once a fixed amount of
motifs have been found. With the maskR option, low-complexity sequences
(i.e.: “aaaaaa”, “cacacaca”, etc) are ignored during the analysis.


rGADEM is now available in the devel section of bioconductor and should be
available very soon in the release section.


Do not hesitate to contact us directly or through the mailing list if you
have any questions!


Best regards,

Charles Joly Beauparlant.


[1] Mercier E., Droit A., Leping L. et al, 2010, An Integrated Pipeline for
the Genome-Wide Analysis of Transcription Factor Binding Sites from
ChIP-seq.

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