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

[Sole Acha, Xavi]

Clustal may work for you.

http://www.clustal.org/

HTH,

Xavi.

------
Xavier Solé Acha
Unitat de Biomarcadors i Susceptibilitat
Unit of Biomarkers and Susceptibility
Institut Català d'Oncologia // Catalan Institute of Oncology
Gran Via de L'Hospitalet 199-203
08907 L'Hospitalet de Llobregat, Barcelona, Spain.
Phone: +34 93 260 71 86 / +34 93 335 90 11 (ext. 3194)
Fax: +34 93 260 71 88
E-mail: x.sole (at) iconcologia.net

-----Mensaje original-----
De: bbb-bounces at bioinformatics.org [mailto:bbb-bounces at bioinformatics.org] En nombre de Dan Bolser
Enviado el: viernes, 14 de mayo de 2010 17:30
Para: General Forum at Bioinformatics.Org
Asunto: Re: [BiO BB] How to create a Transcription binding site profile

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
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>

_______________________________________________
BBB mailing list
BBB at bioinformatics.org
http://www.bioinformatics.org/mailman/listinfo/bbb