We do not have a specific tool for clustering of TFBS. However, if
you know good open source tools that can be used for that purpose we
will consider integrating them into Galaxy framework.
I am just starting to use galaxy, and I was wondering if there is a
simple way to search genome wide for clustering of custom
binding sites (preferentially with weight matrixes). All other
(~10) I have used till so far have their limitations, either the
of the sequence they can handle is rather limited, they use only in
house transcription factor binding sites or they are not able to check
for evolutionary conservation.
Department of Biochemistry and Molecular Biology
Center for Comparative Genomics and Bioinformatics
Penn State University