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.
•
written
by
ZheFrench
1 answer
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.
Log in to answer this question.
-
How toconvert a set of motif consensus sequences in IUPAC to meme format?
written by ilovesuperheroes1993 •
-
Converting motif databases from meme suite to other formats
written by nanoide
-
Convert binding site formats from different databases and compare the motifs - any tools available?
written by JJ
-
MEME result v FIMO result for target annotation
written by BioinfGuru
-
Background letter frequencies
written by sangram_keshari
-
Background file options using the MEME Suite
written by af322 •
-
Make motif position matrix based on multiple sequence alignment.
written by philrees •
-
Position Frequency Matrix to Position Weight Matrix, whose colsums need to be 1.
written by Zhilong Jia
-
How do you convert the motifs databases provided in MEME suite to FASTA format needed for FIMO
written by drautuna •
-
jaspar2meme input file
written by datanerd
