MEME (Multiple EM for Motif Elicitation) is a widely used tool for identifying novel 'signals' in biological sequences, such as transcription factor binding sites and protein domains. It searches for repeated, ungapped sequence patterns in DNA or protein sequences. Users can perform MEME searches via a web server hosted by the National Biomedical Computation Resource (NCBR) and access the Motif Alignment and Search Tool (MAST) to search sequence databases for matches to motifs. The MEME output includes HTML displays of motifs as local multiple alignments and various formats, allowing users to compare motifs with known databases, search for matches in sequence databases, and display motifs in different ways. The article discusses the architecture of the web server, effective use of MEME, and future improvements, including the addition of background sequence models and algorithms for removing low-complexity regions and repeated elements. The MEME web server has seen steady growth in usage since its introduction in 1996, and the authors plan to enhance it further to improve sensitivity and functionality.MEME (Multiple EM for Motif Elicitation) is a widely used tool for identifying novel 'signals' in biological sequences, such as transcription factor binding sites and protein domains. It searches for repeated, ungapped sequence patterns in DNA or protein sequences. Users can perform MEME searches via a web server hosted by the National Biomedical Computation Resource (NCBR) and access the Motif Alignment and Search Tool (MAST) to search sequence databases for matches to motifs. The MEME output includes HTML displays of motifs as local multiple alignments and various formats, allowing users to compare motifs with known databases, search for matches in sequence databases, and display motifs in different ways. The article discusses the architecture of the web server, effective use of MEME, and future improvements, including the addition of background sequence models and algorithms for removing low-complexity regions and repeated elements. The MEME web server has seen steady growth in usage since its introduction in 1996, and the authors plan to enhance it further to improve sensitivity and functionality.