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: [email protected] [mailto:[email protected]] 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] <[email protected]> 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 > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
