Introduction to Computational Molecular Biology:
Genome and Protein Sequence Analysis
(Winter Quarter 2017)
Assignment 1, due Sunday Jan 15
Assignment 2, due Sunday Jan 22
Assignment 3, due Sunday Jan 29
SYLLABUS & LECTURE SLIDES:
Nature paper on Avida
Avida web site
Nature paper on human genome sequence
Nature paper on mouse genome sequence
Siepel et al. paper on PhyloHMMs & sequence conservation
Rabiner tutorial on HMMs
HMM scaling tutorial (Tobias Mann)
Supervised learning tutorial
- Biological Review : Gene and genome structure in prokaryotes and eukaryotes; the genetic code & codon usage; "global" genome organization. Sources and characteristics of sequence data; Genbank and other sequence databases.
- Lecture 1: Course overview.
- Lecture 2: Finding exact matches in sequences using suffix arrays. Algorithmic complexity. Directed graphs. Reading: Durbin et al. section 2.1, 2.2, 2.3.
- Discussion Section 1: HW1 and general programming tips.
- Lecture 3: Depth structure of directed acyclic graphs (DAGs); trees and linked lists. Dynamic programming on weighted DAGs. Reading: Durbin et al. 2.4, 2.5, 2.6.
- Lecture 4: Dynamic programming on weighted DAGs. Maximal-scoring sequence segments. Reading: Durbin et al. 6.1, 6.2, 6.3; Ewens & Grant 1.1, 1.2, 1.12, 3.1, 3.2, 3.4, 3.6, 5.2, 9.1, 9.2
- Discussion Section 2: HW1, HW2, minimum path algorithms, and memoization.
- Lecture 5: Maximal-scoring sequence segments. Reading: Ewens & Grant 5.3.1, 5.3.2, 12.1, 12.2, 12.3; Durbin et al. chapter 3
- Lecture 6: D-segments, relationship to 2-state HMMs. Sequence alignment.
- Discussion Section 3: HW1 comments, HW2 questions, D-segment algorithm, and coding guidelines.
C/C++ PROGRAMMING GUIDES:
OTHER RELEVANT COURSES AT UW:
COMPUTATIONAL BIOLOGY COURSES AT OTHER SITES: