## Specific Information

#### Announcements

The first HW assignment is now posted. It is due by 2pm on Tuesday 27/10/15.
The second HW assignment is now posted. It is due with the final.
#### Class Notes

#### Supplementary Material

A model of evolutionary change in proteins. MO Dayhoff, RM Schwartz, BC Orcutt - Atlas of protein sequence and structure, 1978
Table 22 from Dayhoff et al.: marginal amino acid frequencies
Table from Figure 82 of Dayhoff et al.: scaled transition probability matrix for one step of the PAM chain
Sequences for global alignment exercise in Assignment #1
Forward, backward and Viterbi as well as sampling R functions for HMM
BLOSUM62 marginals
HMM output
#### Staff

#### Schedule

- Lecture in weeks 7-13 (AGR): Tue, Thu 2-3pm
- Office Hours: Mon 4:30pm

#### Grading Structure and Schedule (Uri's half)

- 2 assignments (20% each)
- A take home final (60% of Uri's mark)
- Attendance in classes is required

#### References

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

#### Syllabus

- Pairwise sequence alignment using dynamic programming
- Substitution matrices
- Database similarity search and seeded or hashed alignment
- 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