Learn to use the MEME suite sequence annotation tools FIMO, MAST, GLAM2SCAN and MCAST. The results are emailed to you and are available on the web, and offer extensive computational and schematic details of the motifs it has found, with links to more information and additional analysis features. Each tool uses the input motifs to search selected databases for occurrances of those motifs. FIMO find matches to individual motifs, MAST finds sequences that match a set of motifs, GLAM2SCAN find matches to a gapped motif model and MCAST finds clusters of non-overlapping matches to motifs. Download the MCAST example data file by clicking here.

You will learn:

  • about the background and developers of these tools
  • how to input sequences and run searches using FIMO
  • how to search and understand results at MAST
  • the mechanism to go from a GLAM2 search to GLAM2SCAN results
  • the features of MCAST searches


This tutorial is a part of the tutorial group Motifs and Domains. You might find the other tutorials in the group interesting:

Melina II: A Web-Based Tool for Promoter Analysis

MINT: Molecular Interaction Database

Gibbs Motif Sampler: A motif finder and analysis tool

MDscan: Motif Discovery scan for nucleotide and protein motifs

PROSITE: Database of protein domains, families and functional sites

MEME Suite TOMTOM and GOMO algorithms: Motif discovery tool that can detect conserved motifs in a set of DNA or protein sequences that you provide

MEME Suite GLAM2 Algorithm: Part of a motif discovery tool that can detect conserved motifs in a set of DNA or protein sequences.

MEME Algorithm: Multiple Expectation Maximum for Motif Elicitation

MEME Suite Overview: Motif-based sequence analysis tools

SMART: Protein domain annotation and analysis of domain architectures

InterPro: A comprehensive protein signature resource


Algorithms and Analysis : This category contains various tools that may help perform analysis of different genomics data types. This may include sequence alignment, large-scale or complex queries, motif finding, or comparative assessments.


Video Tip of the Week: Ambiscript Mosaic for visualizing nucleotide motifs: One of the topics I keep an eye on is visualization of various types of genomics data, and I'm always interested in new tools for graphical representations. In the past some of our most popular posts h...

What's the Answer? (promoter identification): BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to...

Tip of the Week: Melina II for promoter analysis: One of the most frequently-asked questions we get when we are out doing workshops is: how do I find motifs in promoters, and what can I do with them to find more information? Just last Friday we were ...

Tip of the Week: MEME Suite of Motif Discovery Tools: In this week's tip I'm going to introduce you to a suite of motif discovery tools, and show you (briefly) how to use one of the tools. The MEME suite is a comprehensive collection of tools for analysi...


Recent BioMed Central research articles citing this resource

Tong Hao et al., Unsupervised statistical discovery of spaced motifs in prokaryotic genomes Prokaryote microbial genomics. BMC Genomics (2017) doi:10.1186/s12864-016-3400-0

Yang Chia-Chun et al., Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data Transcriptomic methods. BMC Genomics (2017) doi:10.1186/s12864-016-3450-3

Aquino Patricia et al., Coordinated regulation of acid resistance in Escherichia coli Empirical systems biology. BMC Systems Biology (2017) doi:10.1186/s12918-016-0376-y

Geuens Thomas et al., Mutant HSPB1 causes loss of translational repression by binding to PCBP1, an RNA binding protein with a possible role in neurodegenerative disease. Acta Neuropathologica Communications (2017) doi:10.1186/s40478-016-0407-3

Amort Thomas et al., Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain. Genome Biology (2017) doi:10.1186/s13059-016-1139-1