Instructor: Vineet Bafna
TA: Nitin Udpa
TR 9:30-10:50am EBU3b 2154
Discussion M:3:00pm WLH 2113
Vineet Bafna: TR 3:30-4:30pm EBU3b(CSE building) 4218
TA Office hours: W2-3, and by appointment
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Midterm 1 will be held in class October 29 (to be confirmed).
|A1 (9/29)||Tues. 10/8 (email TA)||database|
|A2 (10pt)||Tues. 10/20|| Note: For problem 1, run with the following parameters: match:1, mismatch:-3, indel: -2
for Problem 1: human.seq and mouse.seq
for Problem 5: two sequences
|A3 (10pt)||Thurs. 11/5||F1 , F2 , Db , Matrix|
|Project (30pt)|| Checkpoint 1 11/10/2008
Checkpoint 2 11/17
Presentations 12/1, 12/3
Final report 12/7
Rice Proteome (please contact the instructor)
There is no required text for the course. We will use Jones and Pevzner, "An Introduction To Bioinformatics Algorithms", MIT Press, as an optional book.
Future recommended reading is subject to change with little notice. Please note that the available manuscripts are copyright protected, and may be used only for educational purposes. The notes presented here are unedited, and may contain errors. Powerpoint slides are used only to illustrate examples in class, and are not intended to substitute lecture notes.
For Biology, the classic reference Molecular Biology of the Cell is now online, although a bit cumbersome to search. We will link to some of the chapters.
|9/25||Course outline|| L1 |
L1 (pdf of slides)
| Perl 5 guide
Bioinformatics Algorithms web-site
Chap 3 has a brief introduction to Molecular Biology
|9/28||Discussion: Perl/Python Basics||Slides|
|9/29|| Sequence Alignment
| L2 (updated 10/2) |
L2 (pdf of slides)
|Notes on DP|
|10/1|| Dynamic programming variants|
Affine gap costs
L3 (pdf of slides)
Notes: Lin. Space alignment
Xtra credit if you improve
substantially on these notes!
(latex w/out figures)
Historical (fun) notes on SW
Myers-Miller paper intoducing lin. space to bix
Waterman's "Skiing the Sun" (Chapter 4)
|10/6, 10/8|| Space saving alignment
L4 (pdf of slides)
L5 (pdf of slides)
Notes and questions on L4
|10/13|| The Pigeonhole principle |
| L6 |
L6 (pdf of slides)
Notes on Blast Statistics
|10/15||Dictionary matching|| L7
L7 (pdf of slides)
Notes and questions on dictionary matching
Dictionary Matching Notes
|10/20|| Regular Expression Matching |
Protein Sequence Analysis (HMMs)
| L8 |
L8 (pdf of slides)
psi-blast (optional reading)
HMM notes (Only Baum-Welch/Viterbi algorithms were covered)
| L9 |
L9 (pdf of slides)
Transcription and Translation
Ab initio Gene Finding
L10(pdf of slides)
|11/5|| Basics of Mass Spectrometry
L11 (pdf of slides)
|11/10|| Mass Spectrometry |
de novo sequencing
L12 (pdf of slides)
|11/12|| Mass Spectrometry |
L13 (pdf of slides)
|11/17||Microarray data analysis (classification)|| L14 |
L14 (pdf of slides)
|11/19|| Microarray data analysis
| L15 |
L15 (pdf of slides)
|11/24||Genome sequencing|| |
(pdf of slides)
|Final Project Presentation|
We are always looking for motivated students. If you are interested in exploring undergraduate research opportunities in Computational Biology, please email me.