Sequence alignment with respect to a motif
Posted 16 March 2009 - 01:57 AM
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.
Posted 16 March 2009 - 05:36 AM
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
Posted 16 March 2009 - 10:47 PM
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.
Posted 24 May 2009 - 12:18 AM