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CMSC 701: Computational Genomics (Fall 2013) |
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Date |
Topic |
Notes |
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Tuesday, September 3 |
Introduction to class |
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Thursday, September 5 |
Exact matching: intro & KMP algorithm |
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Tuesday, September 10 |
Exact matching: Boyer-Moore |
See text on KMP and Boyer-Moore in Lecture notes Homework 1 (due Monday, 9/16 at midnight) |
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Thursday, September 12 |
Exact matching: multiple pattern – Aho-Corasick |
See text on Aho-Corasick in Lecture notes |
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Tuesday, September 17 |
Exact matching: automata |
See text on automata in Lecture
notes |
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Thursday, September 19 |
Suffix trees: properties |
See text on suffix trees in Lecture
notes Homework 2 - due Tuesday in class |
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Tuesday, September 24 |
Suffix trees: construction with Ukkonen's algorithm |
See text on Ukkonen's algorithm in Lecture notes |
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Thursday, September 26 |
Prof.Tandy Warnow seminar on phylogeny |
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Tuesday, October 1 |
Suffix arrays |
See text on suffix arrays in Lecture notes |
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Thursday, October 3 |
BWT, compressed suffix arrays |
See text on BWT in Lecture notes
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Tuesday, October 8 |
Inexact alignment: dynamic programming variants |
See text on inexact alignment in Lecture notes |
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Thursday, October 10 |
Alignment statistics |
By Dr. Stephen Altschul |
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Tuesday, October 15 |
Alignment statistics |
By Dr. Stephen Altschul |
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Thursday, October 17 |
Midterm |
Dr. Pop out of town |
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Tuesday, October 22 |
More on dynamic programming |
See text on advanced topics in dynamic programming in Lecture notes
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Thursday, October 24 |
Speed-ups/parallel algorithms |
See text on advanced topics in dynamic programming in Lecture notes
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Tuesday, October 29 |
Alignment heuristics |
See text on alignment heuristics in dynamic programming in Lecture notes
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Thursday, October 31 |
Alignment heuristics/spaced seeds |
See text on alignment heuristics/spaced seeds in dynamic programming in Lecture notes
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Tuesday, November 5 |
Chaining algorithms/Multiple sequence alignment |
See text on chaining algorithms/multiple sequence alignment in Lecture notes
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Thursday, November 7 |
Multiple sequence alignment |
See text on multiple sequence alignment in Lecture notes Homework 3: Section 1.4.3.6 - problems 2 and 3, Section 1.4.4.5 - problem 1. Due: midnight, Nov 13.
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Tuesday, November 12 |
Probabilistic alignment, markov models |
See text on multiple sequence alignment in Lecture notes
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Thursday, November 14 |
RNA structure |
See text on RNA structure in Lecture notes
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Tuesday, November 19 |
Motif finding by Stephen Altschul |
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Thursday, November 21 |
Multiple alignment scoring based on Dirichlet mixtures |
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Tuesday, November 26 |
Sequence clustering/Phylogeny |
See text on sequence clustering in Lecture notes
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Thursday, November 28 |
Thanksgiving, no class |
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Tuesday, December 3 |
Sequence clustering/Phylogeny |
See text on sequence clustering in Lecture notes
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Thursday, December 5 |
Sequence assembly |
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Tuesday, December 10 |
Sequence assembly |
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Thursday, December 12 |
Current research topics |
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Monday, December 16 |
8-10am FINAL EXAM |
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