CMSC 701: Computational Genomics (Fall 2014) |
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Date |
Topic |
Notes |
Tuesday, September 2 |
Introduction to class |
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Thursday, September 4 |
Exact matching: intro & KMP algorithm |
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Tuesday, September 9 |
Exact matching: Boyer-Moore |
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Thursday, September 11 |
Exact matching: multiple pattern – Aho-Corasick |
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Tuesday, September 16 |
Exact matching: automata |
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Thursday, September 18 |
Suffix trees: properties |
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Tuesday, September 23 |
Suffix trees: construction with Ukkonen's algorithm |
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Thursday, September 25 |
Suffix arrays |
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Tuesday, September 30 |
BWT, compressed suffix arrays |
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Thursday, October 2 |
Inexact alignment: dynamic programming |
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Tuesday, October 7 |
Inexact alignment: dynamic programming
variants, RNA structure |
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Thursday, October 9 |
Speed-ups/parallel algorithms |
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Tuesday, October 14 |
Alignment statistics |
By Dr. Stephen Altschul |
Thursday, October 16 |
Alignment statistics |
By Dr. Stephen Altschul |
Tuesday, October 21 |
Midterm |
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Thursday, October 23 |
Alignment heuristics |
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Tuesday, October 28 |
Alignment heuristics/spaced seeds |
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Thursday, October 30 |
Chaining algorithms |
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Tuesday, November 4 |
Multiple sequence alignment |
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Thursday, November 6 |
Multiple sequence alignment |
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Tuesday, November 11 |
Motif finding by Stephen Altschul |
Local Multiple Sequence alignment
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Thursday, November 13 |
Multiple alignment scoring based on Dirichlet mixtures |
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Tuesday, November 18 |
Probabilistic alignment, markov models |
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Thursday, November 20 |
Sequence clustering/Phylogeny |
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Tuesday, November 25 |
Sequence clustering/Phylogeny |
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Thursday, November 27 |
Thanksgiving, no class |
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Tuesday, December 2 |
Sequence assembly |
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Thursday, December 4 |
Sequence assembly |
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Tuesday, December 9 |
Testing/Validation |
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Thursday, December 11 |
Current research topics |
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Tuesday, December 16 |
8-10am FINAL EXAM |
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