A motif, also termed a consensus sequence, is a stretch of DNA that has either the exact (rare) or a similar sequence in many places across the genome; you can think of it like input to a fuzzy search, close but not exact, maybe a misspelling or two. These sites often serve as places where proteins physically interact and bind along the DNA. There are data collections, based on sequencing data, that allow one to know where along the DNA that a given protein binds, and from which one may look for enriched or common motifs by looking at the sequence from the binding coordinates. It may be that these motifs are associated with the protein in question, or they may be motifs for other proteins which interact with the protein you have data for. Collections of motifs in a region (such as the promoter region, where many proteins bind to turn a gene on, off, increased, or decreased--think dimmer switch) can be refered to as cis regulatory regions. You know you found one when you can see an enrichment or increased frequency over some background (control) sequence. Common programs used in this analysis are MEME and nestedMICA. Does this help a bit?
In reply to Re^3: genetic algorithm for motif finding
by bioinformatics
in thread genetic algorithm for motif finding
by shakehands
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