Class Notes
| Date | Class Powerpoints and Readings | Scribe Notes |
|---|---|---|
|
The Regulatory Genome - Intro [PPT] [PDF] Genome Assembly - Intro [PPT] [PDF] Gold Bug and Margaret Dayhoff [PPT] [PDF] Also, check the resources page for introductories to molecular biology and the complete Gold Bug story. |
||
Alignment - Intro [PPT] [PDF] Optional reading handed out in class |
[PDF] | |
Statistical Significance for Sequence Analysis [PPT] [PDF] Suggested Readings |
[PDF] | |
Solution to the Monty Hall Problem [PPT] [PDF] Suggested Readings |
[PDF] | |
| Local Alignment Class 5 - 2/10/11 | Readings Storytelling about Lighthouses: When Professor Dijkstra Slapped Me in the Quest for Beautiful Code A note on two problems in connexion with graphs |
[PDF] |
| Substitution Matrices Class 6 - 2/15/11 | Readings A model of evolutionary change in proteins Amino acid substitution matrices from protein blocks |
[PDF] |
| Dayhoff Scoring Matrices and Information Theory Class 7 - 2/17/11 | Readings Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes |
[PDF] |
| Affine Gap Penalties and the Hirschberg Algorithm applied to Sequence Alignment Class 8 - 2/24/11 | Readings Sequence alignment in linear space |
[PDF] |
| Alignment Statistics and the Hirschberg Algorithm Class 9 - 3/1/11 | Class 9 [PDF] | |
| Genome Assembly Class 10 - 3/3/11 | Readings Idury and Waterman. A New Algorithm for DNA Sequence Assembly Pevzner and Waterman. An Eulerian path approach to DNA fragment assembly |
Class 10 and 11 [PDF] |
| Class 11 - 3/8/11 | ||
| Class 12 - 3/10/11 | Class 12 [PDF] | |
| Class 13 - 3/15/11 | Class 13 [PDF] | |
| Class 14 - 3/17/11 | Class 14 [PDF] | |
| Class 15 - 3/22/11 | Class 15 and 16 [PDF] | |
| Class 16 - 3/24/11 | Readings Distribution Handout Initial sequencing and analysis of the human genome The sequence of the human genome Whole genome shotgun assembly and comparison of human genome assemblies |
|
| Class 17 - 4/5/11 | ||
| Class 18 - 4/7/11 | ||
| Class 19 - 4/12/11 | ||
| Class 20 - 4/14/11 | HMM 1 [PDF] | |
| Class 21 - 4/19/11 | ||
| Class 22 - 4/21/11 | ||
| Class 23 - 4/26/11 BLAST |
BLAST 1 [PDF] | |
| Class 24 - 4/28/11 BLAST |
BLAST 2 [PDF] | |
| Class 25 - 5/5/11 Compressiong Algorithms: Suffix Trees and Burrow-Wheeler transfrom |
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| Optional Class 26 - 5/6/11 at 1:00 PM Compression Algorithms: Suffix Trees and Burrow-Wheeler transfrom |
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| Class 27 - 5/10/11 Regulatory Genomics |
PWM [PDF] Final Exam available for pickup during regular business hours at Angel Murakami's office (cubicles between elevators) until May 17. |
|
| Final Exam Period (Final Project Presentations) - 5/16/11 at 9:00am Compression Algorithms: Suffix Trees and Burrow-Wheeler transfrom |