Class 14: Gene Prediction (2)

Back to Gene Prediction (1). On to Mid-Semester Examination.

This outline is also available in PDF.

Held: Tuesday, 11 October 2011

Summary: We continue our exploration of gene prediction by considering a relatively new technique for gene prediction. We prepare for the upcoming mid-semester examination.

Related Pages:

EBoard.
Reading: Chapter 6.
Due: Reading response: Kellis et al. 2003.

Notes:

Don't forget that Project 6.5 is due on Thursday.
Don't forget that the exam is on Thursday!
EC for Panel Discussion on the Future of the Book, Thursday, 4:15, in Faulconer.
EC for Volleyball Friday at 7:00 p.m. in Darby.
EC for Volleyball Saturday at 11:00 a.m. and 3:00 p.m. in Darby.

Overview:

Kellis et al. 2003.
Exam Policies.
Exam Review.
Questions on Sample Exam.

Discussion of Kellis et al. 2003

A few initial questions:

Why is S. cerevisiae used as a model organism?
What do you see as the important results of this paper?
What pre-existing algorithms do the authors rely upon?

Exam Format

Thursday's exam.

In class.
No computer. (We discussed it, and time to solve computer-based problems seems remarkably inconsistent.)
You may bring one page of notes. (8.5x11, double sided.)
Designed to take about ninety minutes, so that you'll have enough time.
For Python: You will not need to write working code. You may need to read code. You may need to write code. You may need to explain how to modify code.
About six problems (some with subproblems).

Review Format

The exam is based on the first six chapters of our textbook, and the four sets of readings that we've done (Dinosaur DNA, HIV, BLAST, Kellis).
Rather than giving you a list of topics, we'll start by going around the room, identifying and categorizing topics that we've studied this semester.
Praitis and Rebelsky will fill in any topics they think are missing.
We'll then continue by discussing any of the topics for which you feel you need some review.

Primary Categories:

Biological Frameworks
Key Bioinformatics Algorithms
Bioinformatics Tools (e.g., at NCBI)
Programming in Python
Research Papers

Questions on the Sample Exam

Are there questions you have on the sample exam?

Back to Gene Prediction (1). On to Mid-Semester Examination.

[Skip to Body]
Primary: [Front Door] [Schedule] - [Academic Honesty] [Instructions] - [ExBioPy]
Current: [Current Outline] [Current EBoard] - [Current Assignment] [Current Lab]
Groups: [Assignments] [EBoards] [Examples] [Handouts] [Labs] [Outlines] [Readings]
Misc: [SamR] [Textbook] [NCBI] [SMS] [BIO/CSC 295 2009F]

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.

This document was generated by Siteweaver on Tue Nov 22 13:06:02 2011.
The source to the document was last modified on Mon Aug 22 11:16:57 2011.
This document may be found at http://www.cs.grinnell.edu/~rebelsky/Courses/CSC295/2011F/Outlines/outline.14.html.

You may wish to validate this document's HTML ; ;

Samuel A. Rebelsky, rebelsky@grinnell.edu

Copyright © 2009-2011 Vida Praitis and Samuel A. Rebelsky. This work is licensed under a Creative Commons Attribution-NonCommercial 2.5 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc/2.5/ or send a letter to Creative Commons, 543 Howard Street, 5th Floor, San Francisco, California, 94105, USA.