[BioC] cosmo: how to search for more than one possible TFBS

[Thierry Janssens]

Dear BioConductor,

I am using the cosmo package in oder to screen promoter alleles and the 
promotors of co-regulated genes for conserved motifs.
By the main approach described in the reference manual (and using TCM as 
the model), only a single PWM is generated. But I am interested in the 
occurence of other motifs as well.
Is it possible in cosmo (/like metioned for MEME in *D'haeseleer, P.* 
(2006) How does DNA sequence motif discovery work? /Nature 
Biotechnology/ 24, 959 - 961/) to mask already defined motifs  in a 
consecutive scan?

kind regards,


Thierry

-- 
Thierry K.S. Janssens
Vrije Universiteit Amsterdam
Faculty of Earth and Life Sciences
Institute of Ecological Science
Department of Animal Ecology,
De Boelelaan 1085
1081 HV AMSTERDAM, The Netherlands
Phone: +31 (0)20-5989147
Fax: +31 (0)20-5987123
thierry.janssens at ecology.falw.vu.nl