This site is subject to update through the term. This page was last modified Wednesday Aug 28, 2009.
Time: MW 11:05am-12:20pm
Place: Swearingen 2A22
Syllabus
Textbook: "An Introduction to
Bioinformatics Algorithms" by N. C. Jones and P. A.
Pevzner.
Supporting website: http://bioalgorithms.info
| Date |
Topics |
Slides |
| 08/21/09 |
Introduction (Chapter 1),
Introduction to Algorithms (Chapters 2.1-2.4) |
Lectures 1-2 |
| 08/24/09 |
Asymptotic Time Complexity
(Chapters 2.7-2.8) |
|
| 08/26/09 |
Recursive and Iterative
Algorithms (Chapters 2.5-2.6) |
Lectures 3-4 |
| 08/31/09 |
Algorithm Design Techniques,
Problem Solving (Chapters 2.9-2.12) |
|
| 09/02/09 |
Structure of DNA (Chapters
3.1-3.5) |
Lectures 5-6 |
| 09/09/09 |
RNA and proteins machinery, DNA
analysis, Speciation (Chapters 3.6-3.11) |
|
| 09/14/09 |
Restriction mapping problem,
Partial Digest problem (Chapters 4.1-4.3) |
Lecture
7 |
| 09/16/09 |
Motif Finding Problem, Profiles,
Median Search Problem (Chapters 4.4-4.6) |
Lectures 8-9 |
| 09/21/09 |
Search Trees, Branch and Bound
Algorithms for MFP and MSP (Chapters 4.7-4.9) |
|
| 09/23/09 |
Genome Rearrangements, Sorting
by Reversals (Chapters 5.1-5.4) |
Lectures 10-11 |
| 09/28/09 |
Sorting Signed Permutations,
Problems Solving |
|
| 09/30/09 |
Sequence Alignment, LCS, Edit
Distance (Chapters 6.1-6.5) |
Lecture
12 |
| 10/05/09 |
Local and Global Alignments
(Chapters 6.6-6.9) |
Lecture
13 |
| 10/07/09 |
Multiple Alignment (Chapter 6.10) |
Lecture
14 |
| 10/12/09 |
Gene Prediction: Statistical
Approaches (Chapters 6.11-6.12) |
Lecture
15 |
| 10/14/09 |
Similarity-base Approaches,
Spliced Alignment (Chapters 6.13-6.14) |
Lecture
16 |
| 10/19/09 |
Midterm |
|
| 10/21/09 |
Problem solving, Divide &
Conquer approach to Sorting (Chapter 7.1) |
Lectures 17-18 |
| 10/26/09 |
Space Efficient and
Sub-quadratic Time Alignments (Chapters 7.2-7.4) |
|
| 10/28/09 |
Shortest Super String Problem,
Sequencing by Hybridization (Chapters 8.1-8.8) |
Lectures 19-20 |
| 11/02/09 |
Fragment Assembly in DNA
Sequencing (Chapter 8.9) |
|
| 11/04/09 |
Peptide Sequencing, Spectrum
Graphs (Chapters 8.10-8.12) |
Lectures 21-22 |
| 11/09/09 |
Spectral Convolution, Spectral
Alignment (Chapters 8.13-8.15) |
|
| 11/10/09 |
Exact Pattern Matching, Keyword
and Suffix Trees (Chapters 9.1-9.5) |
Lectures 23-24 |
| 11/11/09 |
Approximate Pattern Matching,
BLAST (Chapters 9.6-9.8) |
|
| 11/16/09 |
Gene Expression Analysis,
Clustering Algorithms (Chapters 10.1-10.4) |
Lecture
25 |
| 11/30/09 |
Evolutionary Trees
reconstruction (Chapters 10.5-10.9) |
Lectures 26-27 |
| 12/04/09 |
Small and Large Parsimony
Problems (Chapters 10.10-10.11), Review |