[BiO BB] How to create a Transcription binding site profile

Maximilian Haussler maximilianh at gmail.com
Mon May 17 17:39:24 EDT 2010


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 <harry.mangalam at uci.edu>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
> >
> > _______________________________________________
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> > BBB at bioinformatics.org
> > 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.
>
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