Question: Use PWM from CISBP-rna to find motif with MEME (FIMO)
2
gravatar for ZheFrench
3.2 years ago by
ZheFrench310
France
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 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.

motif meme cisbp • 1.6k views
ADD COMMENTlink modified 16 months ago by biofalconch470 • written 3.2 years ago by ZheFrench310
0
gravatar for biofalconch
16 months ago by
biofalconch470
Mexico
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:

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.

ADD COMMENTlink written 16 months ago by biofalconch470
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2560 users visited in the last hour
_