BIOL 221T Motifs Study Guide

DNA sequence motif

recurring functionally associated pattern vs. a single invariant sequence

• recurring functionally associated pattern:

• single invariant sequence:

Explain why an exact-match search can miss functional sites and also identify chance matches

Relate motif location to gene structure and function

Explain why a consensus nucleotide is the most frequent choice at a position

Explain what information a position frequency matrix (PFM) provides

Interpret the log-odds scores relative to a background model; explain what positive, negative, and zero scores indicate

Explain how motif scanning examines windows across a sequence. Why might the scanner also need to search the reverse-complement strand?

Interpret sequence logos

Explain the assumptions and limitations of consensus sequences and PWMs, including positional independence