The MEME Suite is a comprehensive web server that facilitates the discovery and analysis of sequence motifs, such as DNA binding sites and protein interaction domains. It includes the popular MEME motif discovery algorithm and the GLAM2 algorithm for discovering motifs with gaps. The suite offers three sequence scanning algorithms—MAST, FIMO, and GLAM2SCAN—to search numerous DNA and protein sequence databases for motifs. Transcription factor motifs can be compared with motifs in various databases using TomTom, and their potential functions can be further analyzed by associating them with Gene Ontology (GO) terms using GOMO. The MEME Suite provides sequence LOGOS for each discovered motif and allows users to submit motifs to additional analysis tools. All tools are implemented as web services via Opal, and the software is freely available for noncommercial use. The suite supports a wide range of motif analysis tasks, including motif discovery, motif-database searching, sequence-database searching, and function assignment, making it a powerful tool for bioinformatics research.The MEME Suite is a comprehensive web server that facilitates the discovery and analysis of sequence motifs, such as DNA binding sites and protein interaction domains. It includes the popular MEME motif discovery algorithm and the GLAM2 algorithm for discovering motifs with gaps. The suite offers three sequence scanning algorithms—MAST, FIMO, and GLAM2SCAN—to search numerous DNA and protein sequence databases for motifs. Transcription factor motifs can be compared with motifs in various databases using TomTom, and their potential functions can be further analyzed by associating them with Gene Ontology (GO) terms using GOMO. The MEME Suite provides sequence LOGOS for each discovered motif and allows users to submit motifs to additional analysis tools. All tools are implemented as web services via Opal, and the software is freely available for noncommercial use. The suite supports a wide range of motif analysis tasks, including motif discovery, motif-database searching, sequence-database searching, and function assignment, making it a powerful tool for bioinformatics research.