Using Bioinformatics to Study Evolution: reading assignments

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Sandra Porter
i-8295f915da92d0ca11a67cd144057d90-rhodies.jpgThe first research assignment for our Alaska NSF Chautauqua course has been posted. Your task is to find a wound-inducible plant gene, learn something about it, and post a description in the comment section. We've already had one excellent answer, but I know there are at least 54 wound-inducible genes, so I expect to see more. Once we get our genes in order (and possibly before), we'll talk more about designing an experiment for detecting gene expression. In the meantime, I have some pre-course reading assignments to help you prepare.


READINGS 1. "Having a BLAST with bioinformatics (and avoiding BLASTphemy)" Alexander Pertsemlidis and John W Fondon III, Eugene McDermott, Genome Biology 2001 2:reviews2002.1-2002.10
A very nice, well-written, introduction to BLAST.
2. Baldauf, SL. Phylogeny for the Faint of Heart: a tutorial (PDF).
An excellent introduction to making phylogenetic trees.
3. "How to make a phylogenetic tree."
This reference comes from the Los Alamos National Laboratory HIV sequence database. It includes a very nice discussion of tree-building methods along with some great diagrams that show common mistakes in preparing trees. This article also compares different programs for making phylogenetic trees. New versions have been released for some of these programs (like MEGA), since this was written, and they may have improved over the versions that were reviewed.
4. The DOE primer on genomics and the genome project.
A classic reference, updated in 2003, that provides an overview of the genome project and defines many of the terms. If you don't know what ESTs, STSs, or contigs are, this is a great place to begin.
Last, there's a book that I really like by Barry Hall that has step by step instructions for making trees and some good background information too. It's called: "Phylogenetic Trees Made Easy." I noticed on Amazon that a new version is coming out towards the end of June, so you may want to wait until after the class to get a copy.

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