Tony: 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. Thanks, anton

Hello,

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 transcription binding sites (preferentially with weight matrixes). All other programs (~10) I have used till so far have their limitations, either the length 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.

Thanks,

Tony

Anton Nekrutenko Asst. Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics Penn State University anton@bx.psu.edu http://nekrut.bx.psu.edu 814.865.4752