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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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.

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