Computational Challenges in Bioinformatics (2016–2017)
Peter Dawyndt, Jan Fostier · Universiteit Gent
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RegisterWeek 07: hidden Markov models
Solve the exercises of the HMM track on Rosalind. In the mean time, we will convert these exercises to Dodona with newly generated test cases and sometimes with some slight modifications to the problem statement. 24 hours before the deadline (next lecture) you will receive an email with the exercise whose solution you’ll have to present in class. You might find some inspiration about using HMM in the following Jupyter Notebook demos:
| Title | Class progress | ||
|---|---|---|---|
| Probability of a hidden path | |||
| Probability of an outcome given a hidden path | |||
| Viterbi decoding | |||
| Outcome likelihood |
Superimposing the symbols of one string over those of another (with gap symbols inserted into the strings) to represent insertions, deletions, and substitutions between the strings.
| Title | Class progress | Status | |||
|---|---|---|---|---|---|
| Counting point mutations | |||||
| Transitions and transversions | |||||
| Consensus and profile | |||||
| Creating a distance matrix | |||||
| Pairwise global alignment | |||||
| Suboptimal local alignment | |||||
| Global multiple alignment | |||||
| Edit distance | |||||
| Edit distance alignment | |||||
| Counting optimal alignments | |||||
| Global alignment with scoring matrix | |||||
| Global alignment with constant gap penalty | |||||
| Local alignment with scoring matrix | |||||
| Maximizing the gap symbols of an optimal alignment | |||||
| Multiple alignment | |||||
| Global alignment with scoring matrix and affine gap penalty | |||||
| Overlap alignment | |||||
| Semiglobal alignment | |||||
| Local alignment with scoring matrix and affine gap penalty | |||||
| Isolating symbols in alignments |