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

[ocean]

MEME could work.




在2010-05-14，"Martin Gollery" <marty.gollery at gmail.com> 写道：
>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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