1. Refresh your knowledge of pHMMs by reproducing the R package 'aphid' vignetteexercise (link from previous week).

    A nice formal write-up for general HMMs and the terminology and algorithms involved (WILL ADD LINK)

2. Can you create a HMM (either profile or general) that would generate sequences likely to form G-quadruplexes?

    G-quadruplex is a sequence containing 4 runs of Gs, each of ideally 3Gs and a short loop section with no special sequence preferences (may not be entirely true in real G4s). Sometimes a regular expression G3+N+G3+N+G3+N+G3+ is used to identify PQS sequences (PQS = potential quadruplex sequence), or R package pqsfinder can be used.

3. Profile HMM exercise using HMMER

http://www.math.chalmers.se/Stat/Bioinfo/Master/Courses/BioinformaticsII/HMM_lab.html