CS Grade Server (grades.cs.umd.edu)
Date |
Topics |
Slides/Lecture notes |
Add'l resources |
09/01 |
Introduction |
|
|
09/03 |
Molecular biology primer |
Bio-Introduction |
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09/08 |
Molecular biology primer - PCR, sequencing Programming for Bioinformatics |
Homework 1 due Bio-Programming,
utilities |
www.bioperl.org |
09/10 |
Bioinformatics Databases |
Homework 2 (Project part 1) Bio - Databases |
|
09/15 |
Sequence alignment - exact matching |
Admin notes |
|
09/17 |
Sequence alignment - exact matching |
Homework 2 due Lecture 6 |
KMP
algorithm: http://www.ics.uci.edu/~goodrich/dsa/11strings/demos/pattern/ http://www-igm.univ-mlv.fr/~lecroq/string/ http://www.cs.ubc.ca/labs/beta/Courses/CPSC445-08/Handouts/kmp.pdf |
09/22 |
Suffix trees |
Exact
matching: suffix trees |
|
09/24 |
Suffix arrays Data compression |
Lecture 8 |
|
09/29 |
Suffix trees/arrays & midterm recap |
|
|
10/01 |
Midterm 1 |
basic biology + exact matching |
|
10/06 |
Sequence alignment - inexact matching |
Inexact
alignment Dr. Pop out of town |
|
10/08 |
Midterm recap |
Alignment heuristics Chap. 6 |
|
10/13 |
Sequence alignment - inexact matching |
|
|
10/15 |
Sequence alignment - inexact matching, affine gaps |
|
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10/20 |
Sequence alignment heuristics Chaining algorithms |
Project part 2 due |
|
10/22 |
Multiple sequence alignment Motif finding |
Chap. 6.7 |
ClustalW |
10/27 |
Genome sequence assembly |
Genome
assembly |
|
10/29 |
Genome sequence assembly |
|
|
11/03 |
Phylogenetic trees Tree analysis/display |
Chapter 12 Project part 3 due |
|
11/05 |
Midterm 2 |
|
|
11/10 |
Phylogenetic analysis |
|
|
11/12 |
Genetic association studies |
Chap. 13 |
|
11/17 |
Genetic association studies |
|
|
11/19 |
"Signal" finding Hidden Markov Models |
not in book |
|
11/24 |
Data clustering |
Chap. 11.1-11.6 |
|
11/26 |
Thanksgiving |
no class |
|
12/01 |
RNA structure prediction |
not in book |
|
12/03 |
What you missed... |
Final project due!!! |
|
12/08 |
Recap |
|
|
12/10 |
Recap/Review |
|
|
12/14 |
Final exam |
CSIC 1121, 8-10am |
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