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