Sequence alignment with respect to a motif - (Mar/16/2009 )

Hello All,

I am interested in the nearby region (500 bp either side) of a transcription factor binding motif. I know the genes that transcription factor binds to. I would like to take that 1kb region and align with respect to the transcription factor binding motif i.e. the motif remains at the centre and then the rest of the alignment should take place.

Does anybody know any program that can do this?

Thanks in advance.

Hey

Not an expert at this but this is what I think:

You should take all yr sequences together and do a multiple sequencing alignment. This should align yr motif in all sequences and also align the flanking sequences. However, if this doesn't work, you can take the sequences N-terminus of yr motif and align them, then do the same for sequences whcih are C terminus. Now you have alignment across the motif.

Take it with a word of caution, i am not sure if this is the right way to go about it. But its an idea for sure

Hope it helps

Best
TC

Thanks TC,
I did think in the same way but I wasn't too sure either so thought of putting this question to the fellow folks.

If anyone has any other idea or know how to do it, pleas drop the line.

You should do a multiple sequence alignment and then manually edit the alignment to check that it has been done to match your specific interests, i.e. that the transcription factor binding motif is aligned the way you want it. All of this can be done using Geneious www.geneious.com

RSA Tools, http://rsat.ulb.ac.be/rsat/genome-scale-dna-pattern_form.cgi
has a feature somewhat similar to this which might be useful to you.