MEME Suite

The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses. It includes tools such as meme, meme-chip, fimo, tomtom and mast.

• MEME Suite
  • License
  • Available
  • Usage
  • Support
  • More information

License

The MEME Suite is free for non-commercial and academic use. See the MEME Suite copyright and license.

Available

• Roihu: 5.5.7, via the bio-apps module.

Usage

MEME Suite is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the MEME module:

module load bio-apps/v202603
module load meme/5.5.7

For example, to discover motifs with meme:

meme sequences.fasta -dna -oc meme_out -nmotifs 5

meme is MPI-enabled and can be parallelized across several processes. Below is an example batch job using MPI:

#!/bin/bash
#SBATCH --job-name=meme
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=8
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load meme/5.5.7

meme sequences.fasta -dna -oc meme_out -nmotifs 5 -p $SLURM_NTASKS

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information

• MEME Suite home page

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