I don't know anything specific, but you could try using 'Gibbs sampling' algorithms to automatically discover the motif in the sequence sets?
On 13 May 2010 21:02, Che, Anney (NIH/NCI) [E] <[email protected]> wrote: > > Hi everyone, > > I have questions regarding on how to create a transcription binding sites > profile. > > Since I have the sequences of the areas that bind to the gene from Chip-ChIp > , I can align all the sequences then with the alignment that created to > generate a profile. > > Since this is high-throughput, does any one know any tool that can align > short sequences programmatically and then output an alignment file? > > Also a program that generates an alignment profile from an alignment. > > > Thanks, > > Anney > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
