CMSC 701: Computational Genomics (Fall 2014)

Lecture Notes




Date

Topic

Notes

Tuesday, September 2

Introduction to class

Lecture 1

Thursday, September 4

Exact matching: intro & KMP algorithm


Tuesday, September 9

Exact matching: Boyer-Moore


Thursday, September 11

Exact matching: multiple pattern Aho-Corasick


Tuesday, September 16

Exact matching: automata


Thursday, September 18

Suffix trees: properties


Tuesday, September 23

Suffix trees: construction with Ukkonen's algorithm


Thursday, September 25

Suffix arrays


Tuesday, September 30

BWT, compressed suffix arrays


Thursday, October 2

Inexact alignment: dynamic programming


Tuesday, October 7

Inexact alignment: dynamic programming variants, RNA structure


Thursday, October 9

Speed-ups/parallel algorithms


Tuesday, October 14

Alignment statistics

By Dr. Stephen Altschul
Lecture slides

Thursday, October 16

Alignment statistics

By Dr. Stephen Altschul
Lecture slides

Tuesday, October 21

Midterm


Thursday, October 23

Alignment heuristics


Tuesday, October 28

Alignment heuristics/spaced seeds


Thursday, October 30

Chaining algorithms


Tuesday, November 4

Multiple sequence alignment


Thursday, November 6

Multiple sequence alignment


Tuesday, November 11

Motif finding by Stephen Altschul

Gibbs Sampling

Local Multiple Sequence alignment

Thursday, November 13

Multiple alignment scoring based on Dirichlet mixtures

Dirichlet mixtures

Tuesday, November 18

Probabilistic alignment, markov models


Thursday, November 20

Sequence clustering/Phylogeny


Tuesday, November 25

Sequence clustering/Phylogeny


Thursday, November 27

Thanksgiving, no class


Tuesday, December 2

Sequence assembly


Thursday, December 4

Sequence assembly


Tuesday, December 9

Testing/Validation


Thursday, December 11

Current research topics


Tuesday, December 16

8-10am FINAL EXAM