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

[Harry Mangalam]

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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Harry Mangalam - Research Computing, NACS, Rm 225 MSTB, UC Irvine
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