Statistical Methods in Bioinformatics
Semester 2, 2011

Announcements

• The final will be emailed at 10am on 16/11 and will be due 24 hours later.
• The fifth and last HW assignment is now posted. It due on Thursday 27/10.
• Class notes are available (last updated 27/10)
• Supplementary material is available (last updated 16/11)

Staff

• Lectures: Uri Keich

Schedule

• Lecture (Carslaw 829 - GRID room): Tue 2-3pm
• Lecture (Carslaw 829 - GRID room): Thu 12-1pm
• Office Hour (Carslaw 821): Mon 5:30pm

Grading Structure and Schedule

• Roughly 5 assignments (50% of the course grade)
• A final (50% of the grade)

References

• Richard Durbin et al. Biological Sequence Analysis
• Warren Ewens, Gregory Grant Statistical Methods in Bioinformatics 2nd Edition.

Syllabus

• Biological introduction
• DNA sequencing and the Lander-Waterman model
• Pairwise sequence alignment using dynamic programming
• Substitution matrices
• Database similarity search and seeded or hashed alignment
• The statistical significance analysis of an optimal pairwise alignment (Karlin-Altschul, Dembo-Karlin-Zeitouni)
• Hidden Markov Models
  • Most likely decoding - the Viterbi algorithm
  • Posterior estimation - the forward and backward algorithms
  • Parameters estimation - the Baum-Welch algorithm and the EM algorithm in general
  • Profile HMMs
• Gene finding
• Mass spectrometry: statistical analysis of an optimal PSM