Question: Make motif position matrix based on multiple sequence alignment.
gravatar for philrees
5.6 years ago by
philrees0 wrote:

I have a set of sequences in the form of a multiple sequence alignment. I have generated a Sequence logo image to look for any potential motifs within these set of sequences. I have identified several areas that appear to be relevant. I would like to generate a weighted position matrix of these specific motifs (based on the specific range of bases I have identified) and use this matrix to generate a file that can be used with FIMO to search a database of sequences for that motif.

I know I can use MEME to find the motifs and use that file as my input, however it doesn't seem to find the same motifs as I do because it is not aligning the sequences in the same manner. I have found this post but it doesnt seem to generate them in the correct format.


What is the best way to generate a position matrix for my identified region that is compatible with the MEME suite?


EDIT: Another process that I would be OK with is the following: Use MEME to discover motifs but be able to manually adjust the multiple sequence alignment that it performs before it looks for the motifs. I know based on my own multiple sequence alignment that my sequences do not align on there own as they should.

Thanks in advance

ADD COMMENTlink modified 3.3 years ago by fhsantanna490 • written 5.6 years ago by philrees0

any answer, philrees?

ADD REPLYlink written 3.8 years ago by gustavo.borin0
gravatar for fhsantanna
3.3 years ago by
fhsantanna490 wrote:

ADD COMMENTlink written 3.3 years ago by fhsantanna490
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