MEME could work.
在2010-05-14，"Martin Gollery" <[email protected]> 写道： >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 _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
