Class 17: Structure Prediction (2)

Back to Structure Prediction (1). On to Microarrays (1).

This outline is also available in PDF.

Held: Thursday, 27 October 2011

Summary: We ground our understanding of structure prediction by implementing the standard Chou-Fasman algorithm.

Related Pages:

Overview:

• Discussion: Picking independent projects.
• Programming project: 7.5: Chou-Fasman.

Independent Projects

• The last quarter or so of the semester is devoted to independent projects.
• What is an independent project?
• A group of students (mixed Bio/Non-bio) design and explore a problem in bioinformatics,
• What do we mean by explore?
• Identify and gather an appropriate set of data
• Identify and use existing tools to explore those data
• Build at least one program that will aid in your analysis
• Write a paper that summarizes your results
• What kinds of projects might you do?
• You could extend one of the algorithms we discussed in class
• Implement your own version of BLAST
• Produce a new data set for and improved implementation of Chou-Fasman
• Implement the Kellis algorithm and use it on a different set of data
• You could delve more deeply into data sets from one of our papers
• ...
• Timetable
• Thursday, 12 November: Turn in project proposals
• Tuesday, 17 November: Turn in peer reviews of project proposals
• Thursday, 19 November: Short (five minute) overviews of propoals for visitor
• Tuesday, 24 November, In-class time for working on projects
• Thursday, 26 November, Thanksgiving
• Tuesday, 1 December, In-class time for working on projects
• Thursday, 3 December, Presentations (about fifteen minutes per group)

Programming Project for Chapter 7

• This programming project is also a homework assignment.
• Finish implementing Chou-Fasman.
• Analyze its efficacy on three proteins of your choice. (Should be proteins with a known structure.)
• Find out how people make it better, and describe those improvements

Back to Structure Prediction (1). On to Microarrays (1).

Disclaimer: I usually create these pages on the fly, which means that I rarely proofread them and they may contain bad grammar and incorrect details. It also means that I tend to update them regularly (see the history for more details). Feel free to contact me with any suggestions for changes.

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Samuel A. Rebelsky, rebelsky@grinnell.edu

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