The MEME Suite is a powerful, integrated set of web-based tools for studying sequence motifs in proteins, DNA, and RNA. These motifs encode many biological functions and are important for understanding molecular interactions, including gene regulation. Since its initial description in 2009, the MEME Suite has been expanded with six new tools. It is freely available for academic use at http://meme-suite.org and provides source code for local installation. The MEME Suite includes 13 tools for motif discovery, enrichment analysis, scanning, and comparison. These tools help identify and analyze motifs in DNA, RNA, and protein sequences. The suite includes algorithms like MEME, DREME, GLAM2, MEME-ChIP, CentriMo, AME, SpaMo, and MCAST, each suited for different purposes. For example, MEME is a general-purpose motif discovery algorithm, while MEME-ChIP is designed for large datasets. CentriMo is sensitive to motif position, and SpaMo identifies preferred spacings between motifs. The MEME Suite also provides access to a large number of motif and sequence databases for use in analyses. These databases include in vitro compendia based on SELEX or protein-binding microarrays, as well as human-curated compendia of in vivo or in vitro motifs. The suite's motif comparison tool, Tomtom, allows users to compare motifs discovered by the suite or from literature with a database of motifs. The MEME Suite's web interface provides consistent input forms for its 13 tools, with help bubbles explaining input requirements. Users can input sequences or motifs in various formats, and the suite supports both DNA, RNA, and protein sequence analyses. The suite also allows users to upload their own sequence databases for motif scanning. The MEME Suite has been used in over 9800 published studies and is valuable in a wide variety of scientific contexts. It has been used to make many biological discoveries, including identifying a host-targeting signal in malaria proteins and discovering a protein interaction motif in centromere proteins. The suite also includes tools for analyzing ChIP-seq data, such as MEME-ChIP, which simplifies the analysis of large DNA datasets. The MEME Suite provides extensive user support, including online documentation, an online user forum, and email support. It also includes a variety of tools for motif discovery, enrichment, scanning, and comparison, as well as for analyzing the biological roles of DNA motifs. The suite is widely used in the scientific community for its comprehensive functionality and ability to provide statistically significant results.The MEME Suite is a powerful, integrated set of web-based tools for studying sequence motifs in proteins, DNA, and RNA. These motifs encode many biological functions and are important for understanding molecular interactions, including gene regulation. Since its initial description in 2009, the MEME Suite has been expanded with six new tools. It is freely available for academic use at http://meme-suite.org and provides source code for local installation. The MEME Suite includes 13 tools for motif discovery, enrichment analysis, scanning, and comparison. These tools help identify and analyze motifs in DNA, RNA, and protein sequences. The suite includes algorithms like MEME, DREME, GLAM2, MEME-ChIP, CentriMo, AME, SpaMo, and MCAST, each suited for different purposes. For example, MEME is a general-purpose motif discovery algorithm, while MEME-ChIP is designed for large datasets. CentriMo is sensitive to motif position, and SpaMo identifies preferred spacings between motifs. The MEME Suite also provides access to a large number of motif and sequence databases for use in analyses. These databases include in vitro compendia based on SELEX or protein-binding microarrays, as well as human-curated compendia of in vivo or in vitro motifs. The suite's motif comparison tool, Tomtom, allows users to compare motifs discovered by the suite or from literature with a database of motifs. The MEME Suite's web interface provides consistent input forms for its 13 tools, with help bubbles explaining input requirements. Users can input sequences or motifs in various formats, and the suite supports both DNA, RNA, and protein sequence analyses. The suite also allows users to upload their own sequence databases for motif scanning. The MEME Suite has been used in over 9800 published studies and is valuable in a wide variety of scientific contexts. It has been used to make many biological discoveries, including identifying a host-targeting signal in malaria proteins and discovering a protein interaction motif in centromere proteins. The suite also includes tools for analyzing ChIP-seq data, such as MEME-ChIP, which simplifies the analysis of large DNA datasets. The MEME Suite provides extensive user support, including online documentation, an online user forum, and email support. It also includes a variety of tools for motif discovery, enrichment, scanning, and comparison, as well as for analyzing the biological roles of DNA motifs. The suite is widely used in the scientific community for its comprehensive functionality and ability to provide statistically significant results.