there are hundreds of algorithms to do this. Apart from nmica, you can try trawler: http://ani.embl.de/trawler/
On Fri, May 14, 2010 at 8:56 AM, Harry Mangalam <[email protected]>wrote: > Depends on your output and how you want to process it. If the output > are short reads (10s of bases) as from a HTS technology (Ill, 454, > etc), the output is essentially 'aligned' already - that is the > binding site is effectively encoded in the output. > > If the output is from longer sequences (100s of bases) and you want to > be able to extract the binding sites from those longer sequences to > increase your signal, there are a couple of ways to do it depending > on prior knowledge. > > If you don't know the binding motif, you can use one of the de novo > motif finders such as nmica > <http://www.sanger.ac.uk/resources/software/nestedmica/> to generate > it from the seqs you have. > > If you have a good enough idea of what the sequence is and you can > describe it in a regular expression or IUPAC coding with a few > errors, you can extract the motifs so described plus whatever padding > you want in fasta format using tacg or some other extractor and then > align them using your favorite aligner (clustal, tcoffee, etc). > > hjm > > On Thursday 13 May 2010 13:02:05 Che, Anney (NIH/NCI) [E] 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 > > > > -- > Harry Mangalam - Research Computing, NACS, Rm 225 MSTB, UC Irvine > [ZOT 2225] / 92697 949 824-0084(o), 949 285-4487(c) > MSTB=Bldg 415 (G-5 on <http://today.uci.edu/pdf/UCI_09_map_campus.pdf> > --- > Change is hard; disaster is easy. > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
