Anyone used FIMO from MEME before?

Question

[datanerd]

HI all,

Has anyone used the FImo from MEME suite before?

I have a motif, have the JASPAR ID, Frequency matrix from jaspar. But Iam really having trouble making the required Motif format for FIMO.

Anyone with experience please help!

Thanks in advance!

Mamta

Answer 1

[Alex Reynolds]

The specification for the MEME suite motif input format is located on this page: http://meme.nbcr.net/meme/doc/meme-format.html

They also provide a sample DNA motif input: http://meme.nbcr.net/meme/examples/sample-dna-motif.meme-io

The specification is pretty clear, though I would recommend following it all the way down to line breaks - deviations from the format have caused parsing problems for me, though there have been patches since.