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

[Dan Bolser]

I don't know anything specific, but you could try using 'Gibbs
sampling' algorithms to automatically discover the motif in the
sequence sets?



On 13 May 2010 21:02, 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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