Exercise: Behavior and Limitations of Motif Finding

Today, we’ll look at some behaviors of the popular MEME motif-finding software. MEME is a powerful tool for discovering putative regulatory motifs in DNA sequences. You can find it at http://meme-suite.org/tools/meme. To begin, we’ll focus on a motif-finding problem in D. melanogaster promoter sequences. The sequences we will work with are in the FASTA-formatted file dmel-promoters.fna. These sequences were extracted from just upstream of the transcription start sites of twelve genes, all of which are found on the dot chromosome and exhibit expression specific to fly heads. We hypothesize that these genes, which share both common expression and a common chromosomal environment, are regulated by one or more shared transcription factors.