Jim Thomas, jht
uw.edu (543-7877); Larry Ruzzo, ruzzo
uw.edu (543-6298)Instructors:
Jim Thomas, jhtuw.edu (543-7877);
Larry Ruzzo, ruzzouw.edu (543-6298)
Schedule: Hitchcock 220, TuTh 3:30 - 4:50, Jan. 5 -- Mar. 11.
Final Exam: Hitchcock 220, Th 3/18, 4:30--6:20.
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Links:
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AssignmentsYou are welcome to talk to classmates about principles for solving problems, but do NOT solve specific problems together. In many ways, the problem solving is where you will learn the most for this class, especially the programming.
Problem Set 1
(due Tues. Jan. 12).
All problem sets are due by the start of class on the date listed. TIP - Google your programming problem. For example, "python string search" will get you relevant information on how to search a string pretty easily. Try it for those cryptic error messages, too. |
Test/Demo FilesThe following files are used in some of the in-class exercises and demos.
Sonnet.txt |
| # | Date | Lecture Topic | Programming Topic | Notes & Reading | ||
|---|---|---|---|---|---|---|
| 1 | 01/05 | Overview of course. Introduction to sequence comparison. BLAST, alignment scoring | Slides | Introduction to Python. Interpreter, objects, types, variables, command line | Slides | [1, 2] |
| 2 | 01/07 | Sequence alignment - dynamic programming | Slides | Strings | Slides | |
| 3 | 01/12 | Sequence alignment - local alignment | Slides | Numbers, lists, tuples | Slides | Wikipedia: Smith-Waterman |
| 4 | 01/14 | Sequence alignment - protein score matrices | Slides | File input-ouput, if-then-else | Slides | [3] |
| 5 | 01/19 | Sequence alignment - signficance of similarity scores | Slides | For loops | Slides | Altschul BLAST statistics tutorial |
| 6 | 01/21 | No lecture | While loops and review of programming | Slides | ||
| 7 | 01/26 | Whole genome alignments, Sequence trees - introduction | Slides | More on loops | Slides | |
| 8 | 01/28 | Sequence trees - parsimony and distance | Slides | Dictionaries (hash maps) | Slides | |
| 9 | 02/02 | Sequence trees - distance and maximum likelihood | Slides | Functions, program organization | Slides | Conceptual overview: slide 9; also see Sample Problem #2 |
| 10 | 02/04 | Sequence trees - branch significance, bootstrap | Slides | Sorting | Slides | |
| 11 | 02/09 | Motifs | Slides | Regular expressions | Slides | [4] Regexp: Tutorial; HowTo; Library Ref |
| 12 | 02/11 | Motifs | Slides | Regular expressions | Slides | |
| 13 | 02/16 | Motifs | Slides | Regular expressions | Slides | |
| 14 | 02/18 | BLAST | Slides | Objects | Slides | [5, 6] Reading: Ch 15-18 |
| 15 | 02/23 | Multiple Alignment | Slides | Objects | Slides | [7] Wikipedia: Multiple sequence alignment |
| 16 | 02/25 | Gene Prediction | Slides | Objects | Slides | [8] |
| 17 | 03/02 | Hidden Markov Models | Slides | Biopython | Slides | [9] Biopython, esp Tutorial&Cookbook |
| 18 | 03/04 | Hidden Markov Models | Slides | Biopython | Slides | |
| 19 | 03/09 | Probabilities on pedigrees | Slides | Exceptions | Slides | Wikipedia: Genetic linkage plus the section of Strachan & Read cited therein. |
| 20 | 03/11 | RNA | Slides | Biopython | Slides | Read either [10] or [11] |
Electronic access to journals is generally free from
on-campus computers. For off-campus access, follow the
"[offcampus]" links or look at the
library "proxy server" instructions.
| General
Regular Expressions
"RegExPal" (For Javascript rather than Python, but similar and quite handy. Try it!)
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Biopython
Python Books
Python for Software Design: How to Think Like a Computer Scientist by Allen B. Downey. (Includes early drafts of our text book; cheaper than the published version, but less polished...)
Learning Python by Mark Lutz. O'Reilly (Very comprehensive. Much is accessible to beginners.)
Dive Into Python 3 by Mark Pilgrim. (Another online book. Based on Python 3, so some differences, and more advanced, but also free.)
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James H. Thomas Department of Genome Sciences University of Washington jht uw.edu
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Walter L. Ruzzo |