Instructor: Vineet Bafna
TA: Nitin Udpa
Lectures:
TR 9:30-10:50am EBU3b 2154
Discussion M:3:00pm WLH 2113
Office hours:
Vineet Bafna: TR 3:30-4:30pm EBU3b(CSE building) 4218
TA Office hours: W2-3, and by appointment
Course Information:
Announcements
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MIDTERM:
Midterm 1 will be held in class October 29 (to be confirmed).
ASSIGNMENTS/PROJECT
| Assignment | Due date | Data |
|---|---|---|
| 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 |
Maize Sequence Rice Proteome (please contact the instructor) Augustus GFF |
Lectures
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.
| Lecture | Topic | Slides | Suggested Reading |
|---|---|---|---|
| 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 Local alignment |
L2 (updated 10/2) L2 (pdf of slides) L2 questions | Notes on DP |
| 10/1 | Dynamic programming variants Affine gap costs Linear Space | L3 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 Scoring Matrices |
L4 L5 L4 (pdf of slides) L5 (pdf of slides) Notes and questions on L4 |
Scoring matrices Wiki:Dayhoff |
| 10/13 | The Pigeonhole principle keyword match Blast statistics | L6 L6 (pdf of slides) |
Notes on Blast Statistics
ExPASy tools |
| 10/15 | Dictionary matching | L7 L7 (pdf of slides) Notes and questions on dictionary matching |
Wiki: aho-corasick
Dictionary Matching Notes |
| 10/20 | Regular Expression Matching Profiles Protein Sequence Analysis (HMMs) | L8 L8 (pdf of slides) |
PROSITE psi-blast (optional reading) HMM notes (Only Baum-Welch/Viterbi algorithms were covered) |
| 10/22 | Profiles HMMs |
L9 L9 (pdf of slides) L9 questions | |
| 10/27,28 |
Transcription and Translation
Ab initio Gene Finding Project descriptions |
L10
L10(pdf of slides) |
GENSCAN Twinscan |
| 11/3 | Midterm 1 | ||
| 11/5 | Basics of Mass Spectrometry Isotope Distribution |
L11
L11 (pdf of slides) | Aebersold-Mann Overview |
| 11/10 | Mass Spectrometry de novo sequencing |
L12 L12 (pdf of slides) | |
| 11/12 | Mass Spectrometry Quantitation |
L13 L13 (pdf of slides) | SILAC
Map comparison |
| 11/17 | Microarray data analysis (classification) | L14 L14 (pdf of slides) | |
| 11/19 | Microarray data analysis (dimensionality reduction clustering) |
L15 L15 (pdf of slides) | |
| 11/24 | Genome sequencing | (pdf of slides) | |
| Preview | |||
| Thanksgiving | |||
| Final Project Presentation | |||
Research:
We are always looking for motivated students. If you are interested in
exploring undergraduate research opportunities in Computational
Biology, please email me.