Instructor: Vineet Bafna
TA: Julio Ng
Lectures:
TR 2:00-3:20pm. SOLIS 111
Discussion:M3:00-3:50pm. CENTR201
Office hours:
Vineet Bafna: TR 3:30-4:30pm EBU3b(CSE building) 4218
TA Office hours: By appointment.
Course Information:
Announcements
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Final Exam
Please find it
MIDTERM:
Midterm 1 will be held in class October 26.
ASSIGNMENTS/PROJECT
| Assignment | Due date | Data |
|---|---|---|
| A1 (10pt) | Thurs.,9/28 | db |
| A2 (10pt) | Tues. 10/10 | 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. 10/19 | F1 , F2 , Db , Matrix |
| A4 (10 pt) | 12/7/06 | S1.dta S2.dta Problem 3:data1 Problem 3:data2 |
| Midterm 1 (15pt) | Thurs. 10/26 | |
| project (updated 10/14) | ||
| Checkpoint I (3pt) | Tues., 10/31 | |
| Project Checkpoint II (10pt) | Tues. 11/14 | |
| Final project (17pt) | Thurs. 11/30 |
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 |
|---|---|---|---|
| 9/21 | Course outline | L1 | Perl 5 guide Bioinformatics Algorithms web-site Chap 3 has a brief introduction to Molecular Biology |
| 9/26 | Overview of Hirudo (Prof. Macagno) Sequence Alignment | L2 L2 questions | Hirudo Notes on DP |
| 9/28 | Dynamic programming variants Local alignment Affine gap costs Linear Space | L3 | |
| 10/3 | The Piegeonhole principle Blast Statistics Scoring Matrices | L4 | Notes and questions on L4
Notes on Blast Statistics |
| 10/5 | Dictionary Matching Profiles Regular expression matching Domains | L5 |
Scoring matrices
Dictionary Matching Notes ExPASy tools |
| 10/10 | Protein Sequence Analysis
Pattern matching (Regular expressions) Profiles | L6 |
PROSITE psi-blast (optional reading) |
| 10/12 | Protein Sequence Analysis (HMMs)
Transcription and Translation EST sequencing, EST assembly | L7 L7 questions |
HMM notes (Only Baum-Welch/Viterbi algorithms were covered)
An EST primer |
| 10/17 | Project Outline Ab initio Gene Finding | L8 L8,9 questions | GENSCAN Twinscan |
| 10/19 | DNA signals DNA sequencing | L9 |
MDD
DNA sequencing Lander Waterman Stats |
| 10/24 | No class | ||
| 10/26 | Midterm 1 | ||
| 10/31 | Lander Waterman statistics Shotgun genome assembly | L10 L10 Questions | DNA sequencing Lander Waterman Stats Arachne (A WGS assembler) |
| 11/2 | Basics of Mass Spectrometry Isotope Distribution | L11 | Aebersold-Mann Overview |
| 11/7 | Mass Spectrometry de novo sequencing | L12 | de novo sequencing algorithm |
| 11/9 | Mass Spectrometry Quantitation | L13 | SILAC |
| 11/14 | MS quantitation MS applications Microarray data analysis | L14 | Map comparison |
| 11/16 | Microarray data analysis (classification) | L15 | |
| 11/17 | Microarray data analysis (dimensionality reduction clustering) | L16 preview | |
| 11/21 | Population Genetics Basics | L17 preview | |
| 11/23 | Thanksgiving Holiday | ||
| 11/28 | Population Genetics Basics (possible) | L18 preview | |
| 11/30 | 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.