# MEME Suite

> MEME Suite is an academic bioinformatics software project for discovering and analyzing motifs in DNA, RNA and protein sequences. Its connected web and command-line tools support motif discovery, enrichment, comparison and scanning. Educational, research and nonprofit use is permitted without a fee under its license; commercial licensing is managed by UC San Diego.

- **Founders:** Timothy L. Bailey (Original MEME co-creator; MEME Suite co-developer), Charles Elkan (Original MEME co-creator), William Stafford Noble (MEME Suite co-developer)
- **Products:** MEME, STREME, XSTREME, MEME-ChIP, GLAM2
- **Notable:** Original MEME method described in 1994., MEME web server launched in 1996., The 2009 suite publication documented integrated discovery, scanning, motif comparison and functional-association tools.

## Products & services

- **MEME** — Discovers ungapped motifs using probabilistic models in unaligned DNA, RNA or protein sequences.
- **STREME** — Discovers enriched ungapped motifs relative to control sequences; designed to handle large datasets.
- **XSTREME** — Integrates motif discovery, enrichment, comparison and related analysis for sequences with motifs that may occur anywhere.
- **MEME-ChIP** — Integrates motif analysis for large nucleotide datasets such as ChIP-seq peaks.
- **GLAM2** — Discovers motifs allowing insertions and deletions in DNA or protein sequences.
- **Tomtom** — Compares query motifs against known motif databases.
- **FIMO** — Scans sequences for individual motif occurrences and reports statistical scores.
- **AME** — Tests motif enrichment in sequence sets.
- **Local installation and commercial licensing** — Web interface, command-line tools, Docker distribution, MacPorts installation and source builds; commercial permissions managed by UC San Diego.

## Achievements

- Original MEME method described in 1994.
- MEME web server launched in 1996.
- The 2009 suite publication documented integrated discovery, scanning, motif comparison and functional-association tools.
- The 2015 suite paper reported almost 20,000 unique users in 2014.
- STREME published in 2021 with evaluations using DNA and RNA data.
- Release 5.5.9 published November 22, 2025.

## Latest updates

- **2025-11** — Release 5.5.9 added web-server file-extension validation, MoMo content validation, Tomcat 9.0.107 in the Docker image, a security constraint and database updater fixes.
- **2025-07** — A new NCBI Genomes and Proteins sequence-database category became available.
- **2025-05** — Release 5.5.8 fixed custom-alphabet parsing and other installation and documentation issues; JASPAR CORE 2024 was added earlier that month.

## Links

- Website: https://meme-suite.org/meme/

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Last updated: 2026-10-17