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

[Che, Anney (NIH/NCI) [E]]

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