Question: Use PWM from CISBP-rna to find motif with MEME (FIMO)
gravatar for ZheFrench
3.2 years ago by
ZheFrench310 wrote:

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 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.

motif meme cisbp • 1.6k views
ADD COMMENTlink modified 16 months ago by biofalconch470 • written 3.2 years ago by ZheFrench310
gravatar for biofalconch
16 months ago by
biofalconch470 wrote:

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

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.

ADD COMMENTlink written 16 months ago by biofalconch470
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