GS559 Home Page - Winter 2017

Instructors: Jim Thomas, jht@u.washington.edu; Elhanan Borenstein, elbo@u.washington.edu

TA: Seungsoo Kim, sskim10@u.washington.edu

Tues-Thurs, 10:30-11:50, Hitchcock 220. First class Jan. 3, last class Mar. 9.

Free (legal) PDF text book on Python

Python quick reference guide

Much more extensive python quick reference guide on-line (this will be confusing at first but it is great when you learn a bit more)

Grading Policy

News

Assignments

Problem Set 1, due Tues. 1/17.  Problem Set 1 Answers

Problem Set 2, due Tues. 1/24.  Problem Set 2 Answers

Problem Set 3, due Tues. 1/31.  Problem Set 3 Answers. Files needed for PS3: chr21, blastn_OUT

Problem Set 4, due Tues. 2/7.

Please turn in problem sets on paper in class.

You 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. TIP - Google your programming problem but don't just copy and paste code - write your own.

Lectures and paper links

Reading links should get you a PDF document. Lecture and reading links will be added as the course proceeds.

Lecture 1. Overview of course. Introduction to sequence comparison, alignment scoring. Lecture 1 (PDF).

Programming 1. Introduction to Python. Objects, types, variables, command line. Programming 1 (PDF).

The following articles will become more useful as the course proceeds: Article 1 on bioinformatic skills. Article 2 on bioinformatic skills.

Lecture 2. Sequence alignment - dynamic programming. Lecture 2 (PDF).

Programming 2. Strings. Programming 2 (PDF).

Lecture 3. Sequence alignment - local alignment. Lecture 3 (PDF)

Programming 3. Numbers, lists, tuples. Programming 3 (PDF). sonnet.txt

Lecture 4. Sequence alignment - protein score matrices. Lecture 4 (PDF).

Programming 4. File input-ouput, if-then-else. Programming 4 (PDF).

Lecture 5. Sequence alignment - how blast works. Lecture 5 (PDF).

Programming 5. For loops. Programming 5 (PDF). matrix.txt

Lecture 6. Significance of similarity scores. Lecture 6 (PDF).

Programming 6. While loops. Programming 6 (PDF). small.fasta and large.fasta

Lecture 7. Significance continued. Lecture 7 (PDF).

Programming 7. Loops and efficient code. Programming 7 (PDF). cfam_repmask.txt and cfam_repmask2.txt (huge files - don't try to view in browser!)

More practice on loops (no solutions)

Lecture 8. Whole genome alignments. Lecture 8 (PDF).

Programming 8. Dictionaries (hash maps). Programming 8 (PDF). scores.txt and seq_names.txt

Lecture 9. Sequence trees introduction. Lecture 9 (PDF).

Programming 9. Standard IO. Programming 9 (PDF).

Lecture 10. Unix command line (PDF).