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

Martin Gollery marty.gollery at gmail.com
Fri May 14 11:33:28 EDT 2010


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] <
chea2 at mail.nih.gov> 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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>



-- 
-- 
Martin Gollery
Senior Bioinformatics Scientist
Tahoe Informatics
www.bioinformaticist.biz
www.hiddenmarkovmodels.com



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