uniprobe pwm to meme format

[Ashwini Jeggari]

Hello,

I am using MEME-suite to identify the enriched motifs in my list of DNA sequences.

To run Tomtom and Centrimo, I would like to use input target database file obtained from Uniprobe.

My task is to check if the consensus sites from this publication (link : http://the_brain.bwh.harvard.edu/uniprobe/downloads/GD12/GD12_pwm.zip) are in my input sequences.

The problem is all PWMs files in this file directory are stored as separate folders, and in a different format.

Seems like, a written script to convert uniprobe files to meme format (meme-5.0.1/scripts/uniprobe2meme.pl.in) is already available.

 

I tried to run the script using single file.

perl uniprobe2meme.pl.in uniprobe_Peterson2012_PWM/Gli1/Gli1_v015681/Gli1_v015681_primary.pwm

The output of this script consists of multiple matrices (Enrichment score, probability scores) and a wrong motif name (motif is named as MOTIF PO PO)

Can anyone please guide me through the proper usage of this script, to input PWM files from multiple folders and obtain a single batch file.

 

[CharlesEGrant]

I tried to run the script using single file.
perl uniprobe2meme.pl.in uniprobe_Peterson2012_PWM/Gli1/Gli1_v015681/Gli1_v015681_primary.pwm 

It looks like you are trying to run the template file used to build the uniprobe2meme script rather than the script itself. If you've completed the installation, the script uniprobe2meme will be under libexec/meme-x.y.z, where x.y.z is the version number for the release of the MEME Suite for example

libexec/meme-5.0.2

The documentât for uniprob2meme can be found here.