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Motif Finding

Motif Discovery in Drosophila

This walkthrough uses FlyBase RNA-Seq Search and the MEME suite to discover motifs that are enriched in a collection of D. melanogaster Muller F element genes that show similar expression patterns.

Annotation of Conserved Motifs in Drosophila

This walkthrough uses FlyBase, FlyFactorSurvey, and Patser to identify transcription factor binding sites in the region surrounding the transcription start site of onecut in D. biarmipes.

Behavior and Limitations of Motif Finding

Developed by Dr. Jeremy Buhler, this exercise uses MEME to discover putative regulatory motifs in a collection of D. melanogaster promoter sequences. It also illustrates some of the challenges associated with motif finding and the limitations of motif finding programs.

Introduction to Motifs and Motif Finding

This document contains the notes from a lecture on motif finding given by Dr. Jeremy Buhler in the Bio 4342 course at WU. The lecture covers the different approaches used to represent sequence motifs and to search for sequence motifs in a genome.

Eukaryotic Comparative Genomics

This lecture from Dr. Barak Cohen discusses the major factors to consider (e.g., species to analyze, model for conserved sequences) when using phylogenetic footprinting to identify conserved regions across multiple species. The lecture also illustrates how the weight matrix model can be used to describe sequence motifs, and it provides an introduction to Magma, which uses the multiple species with multiple genes approach to discover conserved motifs.