May 7
Apr 25
Apr 9
Jan 20
Jan 9Class Description
This class is about the major biological problems related to sequence analysis and the algorithms/data structures behind the major bioinformatic tools used to solve them. A solid but not extensive background in coding and statistics are needed. An understanding of the basics of UNIX is also needed. This new version of the course is a hands-on course. The student will be expected to program simple versions of algorithms in the Python programming language. Previous programming experience will be a help but not necessary. The approach will be one of working with executable descriptions of the algorithms to experience their behavior. Discussions of actual implementations and implementation approaches will be covered.
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Time: 2:00-3:15 TTh Final: None Location: JEB 328 |
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Required Text: Biological Sequence Analysis
by Durbin et al. |
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Suggested Text:
The Quick Python Book by Vernon L. Ceder |
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Estimated Syllabus
This syllabus is an estimate of what we might cover this semester based on previous versions of this class.
| Wk# | Monday |
Topics/Links | Assignments | Comments |
|---|---|---|---|---|
| 1 | Jan 12 | How the course works, discussing what students already know | No Class Tues | |
| 2 | Jan 19 | simple frequency stats, dynamic programming and pairwise sequence alignment | NO CLASS ON MONDAY | |
| 3 | Jan 26 | local alignment, scoring matrices | Assignment 1 [pdf], Assignment 2 [pdf] | |
| 4 | Feb 2 | Affine gapping, repeat alignments, BLAST algorithms | ||
| 5 | Feb 9 | Markov Models | ||
| 6 | Feb 16 | Hidden Markov Models | Assignment 3 [pdf] | |
| 7 | Feb 23 | Phylogentic trees, clustering methods | ||
| 8 | Mar 2 | phylogenetic trees distance methods | ||
| 9 | Mar 9 | Phylogentic trees with maximum likelihood. | ||
| 10 | Mar 16 | SPRING BREAK! | NO CLASS THIS WEEK | |
| 11 | Mar 23 | More MCMC | Assignment 4 [pdf] | |
| 12 | Mar 30 | stochastic grammars and RNA structure prediction | ||
| 13 | Apr 6 | more grammars | ||
| xx | Apr 8 | shot gun sequence assembly | Assignment 5 [pdf] | |
| 14 | Apr 20 | more sequence assembly | Assignment 6 [pdf] | |
| 15 | Apr 27 | Genome wide association study algorithms | ||
| 16 | May 4 | Epistasis analysis | ||
| 17 | May 11 | FINAL EXAM WEEK |
References and Resources
Misc References
- slides01.pptx: Basic information about the class and don't forget to read the Policies document attached to this page!
- slides02.pptx: History that lead up to the sequence analysis
- slides03.pptx: A little biology terms to remember
- How to convert from to and from linux and windows formated ascii files
- lib515.py a library of code for simplifying homework assignments. It will in the test environment when your code is run.
- Class notes [pdf]. Some helpful class notes on course content.
Python References
- The Python Library Reference
- The Python Language Reference
- A Python Tutorial
- examples-py.tar are python examples we covered in one of my other classes
LaTeX References
- AMS math guide
- LaTeX for Computer Scientists
- The Giant Book of Symbols
- Cool tool that lets you draw a latex symbol and
it will do pattern matching to look it up. Try it! Don't always pick the first symbol it picks.
- The Source for all things TeX and LaTeX
- examples-tex.tar are the notes I used when I talked about LaTeX in one of my other classes
- A weird LaTeX example just doing lots of things. It requires the files: latexGraph.png, latexHyenaBib.bib, latexStripedHyena.jpg
Services
- Homework submission page. This our homework submission. This is not to be confused with other submission tools used in the CS department.
- Submitting homework without a browser