MEME is a widely used tool for discovering and analyzing DNA and protein sequence motifs. It searches for repeated, ungapped patterns in biological sequences, helping identify transcription factor binding sites and protein domains. Users can access MEME via a web server (http://meme.nbcr.net) and several mirror sites. The tool also allows users to compare discovered motifs with known databases, search sequence databases, and display motifs in various formats. MEME's output includes buttons for further analysis using other web-based programs, such as MAST, which can search sequence databases for matches to motifs. MEME works by searching for statistically significant motifs in input sequences. It automatically determines motif width and occurrence to minimize the 'E-value'—the probability of finding a similar pattern in random sequences. Users can input sequences in FASTA format, and the tool looks for up to three motifs. The tool is suitable for both DNA and protein motifs, with DNA motifs being more challenging due to their short and degenerate nature. For DNA motifs, input sequences should be as short as possible and contain minimal noise. Sequences should ideally be under 1000 bp. Low-information segments can be removed using DUST, and repetitive DNA elements using RepeatMasker. MEME is not suitable for whole-genome TFBS discovery due to the statistical invisibility of short, degenerate motifs. Protein motifs are generally easier to discover due to the length of the protein alphabet and chemical similarity among amino acids. Low-complexity regions can be removed using SEG. MEME can be used to discover protein motifs by following similar guidelines as with DNA motifs. The MEME output includes hyperlinks for further analysis, such as comparing motifs with the JASPAR database or using MAST to search sequence databases. MAST can search for sequences matching motifs found by MEME in various databases, including promoter regions. MEME is available via a web server and can be installed locally. The web server is supported on multiple platforms, including Linux, Solaris, MacOS X, Cygwin, and Irix. The MEME support team provides assistance through forums and mailing lists. Future directions include adding options for background sequence models and integrating workflow tools for grid computing. The authors acknowledge funding from NIH and other sources for the development and maintenance of MEME and MAST. The tool is freely available for academic use, with ongoing support and updates.MEME is a widely used tool for discovering and analyzing DNA and protein sequence motifs. It searches for repeated, ungapped patterns in biological sequences, helping identify transcription factor binding sites and protein domains. Users can access MEME via a web server (http://meme.nbcr.net) and several mirror sites. The tool also allows users to compare discovered motifs with known databases, search sequence databases, and display motifs in various formats. MEME's output includes buttons for further analysis using other web-based programs, such as MAST, which can search sequence databases for matches to motifs. MEME works by searching for statistically significant motifs in input sequences. It automatically determines motif width and occurrence to minimize the 'E-value'—the probability of finding a similar pattern in random sequences. Users can input sequences in FASTA format, and the tool looks for up to three motifs. The tool is suitable for both DNA and protein motifs, with DNA motifs being more challenging due to their short and degenerate nature. For DNA motifs, input sequences should be as short as possible and contain minimal noise. Sequences should ideally be under 1000 bp. Low-information segments can be removed using DUST, and repetitive DNA elements using RepeatMasker. MEME is not suitable for whole-genome TFBS discovery due to the statistical invisibility of short, degenerate motifs. Protein motifs are generally easier to discover due to the length of the protein alphabet and chemical similarity among amino acids. Low-complexity regions can be removed using SEG. MEME can be used to discover protein motifs by following similar guidelines as with DNA motifs. The MEME output includes hyperlinks for further analysis, such as comparing motifs with the JASPAR database or using MAST to search sequence databases. MAST can search for sequences matching motifs found by MEME in various databases, including promoter regions. MEME is available via a web server and can be installed locally. The web server is supported on multiple platforms, including Linux, Solaris, MacOS X, Cygwin, and Irix. The MEME support team provides assistance through forums and mailing lists. Future directions include adding options for background sequence models and integrating workflow tools for grid computing. The authors acknowledge funding from NIH and other sources for the development and maintenance of MEME and MAST. The tool is freely available for academic use, with ongoing support and updates.