The MEME suite of motif-based sequence analysis tools

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Project Summary/Abstract DNA and protein sequences digitally store information about biological function in a complex code that is not yet fully understood. The fundamental unit of this code is the sequence motif, which is defined as a small, recurring DNA or protein sequence pattern. A DNA motif might be involved, for example, in turning on or off the transcription of a gene in response to environmental cues. A protein motif might encode the properties of the binding site that allows the protein to carry out its function. The MEME Suite of motif-based sequence analysis software builds statistical models of DNA and protein motifs, allowing biologists to discover novel motifs, to search for new instances of known motifs, and to compare motifs to one another. This proposal continues to develop and maintain the MEME Suite, which is in regular use by biologists around the world. The aims of this work are five-fold: (1) to increase the accessiblity, usability and interoperability of the MEME Suite, (2) to expand the MEME Suite to handle epigenetic data regarding histone modifications, methylation, nucleosome positioning and DNaseI hypersensitive sites, (3) to integrate a variety of existing motif-based software tools into the MEME Suite, (4) to augment the algorithms used by the MEME Suite with proven enhancements, and (5) to continue to improve our user support services.