Hi Anney, ClustalW will work fine programmatically with short sequences as long as you choose the 'slow, accurate' option.
Best regards, Martin Gollery On Thu, May 13, 2010 at 1:02 PM, 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 > -- -- Martin Gollery Senior Bioinformatics Scientist Tahoe Informatics www.bioinformaticist.biz www.hiddenmarkovmodels.com _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
