Office Hours (EB3134): Thursday 2-3pm, Tuesday 2 - 3 pm, and by appointment
Welcome to the home page for CSE 891. Please find more about this course here.
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9/8/09 The first homework is out today. It is due before the class on 9/22. Read the following homework submission guidelines.
9/8/09 Office hours are updated.
9/8/09 We have four classes for paper presentation (see the table below). The chosen papers will be listed in the "schedule" table. Please pick a time and let me know asap.
Schedule (depending our our progress, this schedule is subject to change. DEKM represents the recommended reference book: biological sequence analysis by R. Durbin, S. Eddy, A. Krogh, and G. Mitchison)
Homework submission guidelines: all the source codes should be submitted via Handin (http://www.secure.cse.msu.edu/handin/). Please make sure your programs can compile and run on arctic.cse.msu.edu, where I am going to test your program. Please write a "readme" file to tell me how to compile your source codes. For non-programming problems, bring your answers to class.
Acknowledgements: some of the source codes and homework problems are provided by Dr. Sean Eddy and Dr. Jeremy Buhler.
| Date | Topic | Notes and Reading | Assigned | Due |
| 9/3 | Intro to Dynamic Programming (DP) and sequence alignment | DEKM 1.1, 2.1,2.1,2.3. More about alignment | ||
| 9/8 | cont. pairwise alignment: scoring models, DP for local alignment | DEKM 2.3, 2.4, 2.8; | HW1 handed out in class. Some helpful source codes. | |
| 9/10 | Heuristic alignment algorithms: BLAST | DEKM 2.7; BLAST | ||
| 9/15 | Karlin-Altschul statistics | DEKM 2.7 K-A theory paper | ||
| 9/17 | Paper presentation | Chiaromonte02: Qiong Eddy-scoringmatrix04: Osama | ||
| 9/22 | Markov chains | DEKM 3 | HW2 is out | HW1; before the class |
| 9/24 | HMM: Viterbi, forward, backward algorithms | DEKM 3. Eddy hmm tutorial | ||
| 9/29 | EM and Baum-Welch for HMM training | DEKM 3 HMM for CpG island finding | ||
| 10/1 | Paper presentation | Using HMM for gene finding: Eden: GeneScan, Nagashri:SLAM, Rayshawn: Human-mouse-gene. | ||
| 10/6 | Sequence family, profile | DEKM 5; More on Dirichlet | HW3 is out | HW2 is due |
| 10/8 | Profile HMM (pHMM) | DEKM 5 | ||
| 10/13 | Algorithms on pHMM | DEKM 5 | ||
| 10/15 | Paper presentation | Using pHMM for protein homology search: Sherine & Shohreh, Edward, Qingpeng | ||
| 10/20 | Guest lecture by Dr. Jin Chen | HW3 is due | ||
| 10/22 | Formal language: regular grammar & context-free grammar | DEKM 9.1, 9.2 | HW4 is out | |
| 10/27 | Stochastic CFG (SCFG) | DEKM 9.3 | ||
| 10/29 | SCFG-based algorithms for ncRNA identification | DEKM 10 | ||
| 11/3 | NcRNA Homology Search Algorithms | HW4.A is due | ||
| 11/5 | Paper presentation | SCFG for ncRNA identification: Yuan Zhang, Stuart, Elijah and Rujira. | ||
| 11/10 | Combinatorial pattern match | HW4.B is due | ||
| 11/12 | Suffix tree | |||
| 11/17 | Suffix tree | |||
| 11/19 | Indexing/filtering for BLAST | |||
| 11/24 | Paper presentation | Algorithms for sequence mapping: Jason, Ling | ||
| 11/26 | No class | |||
| 12/1 | Randomized algorithms for motif finding | |||
| 12/3 | Final project presentation | |||
| 12/8 | Final project presentation | |||
| 12/10 | Final project presentation |