Use PWM from CISBP-rna to find motif with MEME (FIMO)
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Entering edit mode
4.6 years ago
ZheFrench ▴ 460

MEME need a specific matrix for input. The software gives a list of utilities for conversion matrix. For example, you can convert jaspar PFM to MEME matrix input to use with FIMO and find motifs in a sequence.

CISBP-rna http://cisbp-rna.ccbr.utoronto.ca/ let access a list of PWM matrices but I don't see in MEME a conversion Tool for that format. So I was wondering how to use them with fimo or an another tool.

CISBP MEME motif • 2.3k views
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Entering edit mode
2.7 years ago
biofalconch ▴ 510

Maybe a little bit late but here is a workaround I did. You have to transpose the matrix so that it looks like this:

GeneID
A: 0.5  0.5   0
C: 0    0     0.5
G: 0.5  0     0
T: 0    0.5   0.5


I'm not going to post the script since it is a little convoluted but the only thing is to trasnpose, add gene name on top and to add a colon after the nucleotides. Afterwards, using the script uniprobe2meme included in the meme suite and you are good to go.