Make motif position matrix based on multiple sequence alignment.
Entering edit mode
7.0 years ago
philrees • 0

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

position matrix sequence logo sequence alignment • 2.5k views
Entering edit mode

any answer, philrees?

Entering edit mode

Login before adding your answer.

Traffic: 1950 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6