Introduction

The MEME Suite supports motif-based analysis of DNA, RNA, and protein sequences. You can also use it with sequences over novel sequence alphabets that you define. The Suite provides motif discovery algorithms using both probabilistic (MEME) and discrete models (STREME), which have complementary strengths. It also allows discovery of motifs with arbitrary insertions and deletions (GLAM2). The MEME Suite provides three tools for motif enrichment analysis – measuring the enrichment of known motifs in sets of sequences. The motif enrichment may be anywhere in the sequences (SEA, AME), or concentrated in the central regions of the sequences (CentriMo). The Suite also provides an algorithm for measuring the similarity between motifs (Tomtom). These three types of analysis are combined in a pipeline in two MEME Suite tools – XSTREME and MEME-ChIP – that perform comprehensive motif analysis in general sequences (XSTREME) or in ChIP-seq peaks (MEME-ChIP). In addition to motif discovery, the MEME Suite provides tools for scanning sequences for matches to motifs (FIMO, MAST and GLAM2Scan), scanning for clusters of motifs (MCAST), finding preferred spacings between motifs (SpaMo), predicting the biological roles of motifs (GOMo), and predicting the regulatory targets of transcription factors.

For more information, visit the MEME official website.

Programming language: C

Brief description: A tool for motif-based analysis of DNA, RNA and protein sequences.

Open source license: GPL 3.0

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