Multipe Sequence Alignments:
Dealing With Repeats

  1. Identify the various components using blast.

  2. Treat each domain separately.

  3. Scan each domain for repeats.

  4. Build a multiple alignment of the repeats to identify conserved residues.

  5. Use prosite to predict the activity of the various elements.

    • Prosite patterns usually include the active site as an invariant residue.
    • If the active site is mutated, the pattern will not be detected...
    • The only way around is to align the prospective motif with an active homologue...

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