Computing for Bioinformatics Lectures for Fall 2007
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Lecture |
Date |
Topics |
Overheads |
Handouts |
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31 |
Final Exam on Wednesday, December 12, from 1-2:50 PM in ITT 332 |
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30 |
12/6 |
Review for Final |
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29 |
12/4 |
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28 |
11/29 |
Section 7.4: Subquadratic LCS alignment |
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27 |
11/27 |
Section 7.3: Block Alignment Problem using Four-Russians speedup |
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26 |
11/15 |
Section 7.2: Space-Efficient Sequence Alignment |
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25 |
11/13 |
Section 7.1: Merge Sort |
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24 |
11/8 |
Chapter 7: Introduction to Divide-and-Conquer Algorithms: Binary search; Master Theorem for solving recurrence equations |
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23 |
11/6 |
Section 6.13-6.14: Similarity-Bassed Approaches to Gene Prediction, and Spliced Alignment |
Similarity-Bassed Approaches to Gene Prediction, and Spliced Alignment |
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22 |
11/1 |
Section 6.12: Statistical Approaches to Gene Prediction |
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21 |
10/30 |
Section 6.11: Gene Prediction: Regulation of Protein Production, and patterns of substitution within genes. |
Regulation of Protein Production and Patterns of Substituion within Genes |
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20 |
10/25 |
Section 6.10: Multiple Sequence Alignment |
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19 |
10/23 |
Sections 6.7-6.9: Local Alignment, Affine Gap Penalties |
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18 |
10/18 |
Section 6.4-6.6: Edit Distance, Longest Common Subsequence, Global Alignment |
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17 |
10/16 |
Section 6.3 Manhattan Tourist Problem |
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16 |
10/11 |
Section 6.1-6.2: Dynamic Programming: Coin-change, Binomial-coefficient, memoization |
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15 |
10/9 |
Return and Discuss Test 1 |
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14 |
10/4 |
Test 1 |
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13 |
10/2 |
Review for Test 1 |
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12 |
9/27 |
Section 5.3 – 5.4: Approximation Algorithms and ImprovedBreakpointReversalSort Analysis |
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11 |
9/25 |
Section 5.1-5-3: Greedy Algorithms, Sorting by Reversals, Approximation Algorithms |
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10 |
9/20 |
Section 4.8-4.9: Motif Finding Problem – Branch-and-Bound |
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9 |
9/18 |
Section 4.7: Motif Finding Problem, Search Trees |
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8 |
9/13 |
Section 4.4-4.7: Regulatory Motifs in DNA, Profiles, Motif Finding Problem |
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7 |
9/11 |
Sections 4.3 Backtracking Algorithms, Partial Digest Problem |
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6 |
9/6 |
Sections 4.1-4.2 Brute Force Algorithms, Partial Digest Problem |
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5 |
9/4 |
Sections 3.7-3.11: Protein Production, DNA sequencing, Genome Diversity |
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4 |
8/30 |
Sections 3.1-3.6: Central Dogma of Molecular Biology |
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3 |
8/28 |
Sections 2.10-2.11: Big-Oh, Tractable vs. Intractable Problems |
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2 |
8/23 |
Sections 2.5-2.9: Recursion, More Problem-Solving Techniques |
More Problem-Solving Techniques (.ppt)
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1 |
8/21 |
Chapter 1: Intro. To Bioinformatics Sections 2.1-2.4: Intro. To Problem-Solving Techniques |
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