Introduction to Motifs and Motif Finding

• Biologically speaking, a motif in DNA or RNA (or protein) sequence is a short functional sequence element. • Examples found in genomic DNA include – transcription factor binding sites – small noncoding RNAs – small repetitive elements (e.g. inverted repeats) – common mRNA elements, such as Shine-Dalgarno or Kozak sequences, splice enhancers and suppressors. • We will be strongly tempted to talk about conserved DNA sequence motifs. But we must be careful to recognize that many motifs, especially short transcription factor binding sites, are known to arise convergently. Hence, the various instances of a motif, while similar in appearance, may not actually be homologs. Don’t say “conserved” unless you mean it!