Summer 2002. MCB 396. Section 41

Computer Applications in Genomics

June 3 - June 14

Instructor: Olga Zhaxybayeva
Meeting time: 1-5pm
Meeting Place: Mac Lab, LSA 306

Tentative Syllabus:

Session 1 (6/03)	Introduction Recommended Books Databases at NCBI. Using Entrez. Other Databases Common Data Formats of DNA/Protein Sequences Assignment #1 Links: Entrez Nucleic Acid Research Database Issue
Session 2 (6/04)	Addendum to class #1 Overview on Phylogenetic Reconstruction: From Databank Searches to Tree Building; Types of Homology How to detect Open Reading frames, Introns and Exons? Assignment #2 Links: ORFinder@NCBI GeneMachine GeneScan SEQUIN Biologist's WorkBench Table of Standard Genetic Code
Session 3 (6/05)	Addendum to class #2 Homology assessment: When are two sequences homologous? Z-values, PRSS, BLAST and PSI-BLAST. Assignment #3 Links: PRSS BLAST
Session 4 (6/06)	Addendum to class #3 Pairwise and Multiple Sequence Alignments Assignment #4 Links: Dotlet ClustalX
Session 5 (6/07)	Quiz (15 minutes). Addendum to class #4 Intro to Trees Building distance trees with ClustalW, Depicting Trees with TreeView, Neighbor Joining, Bootstrapping Assignment #5 Number of unrooted/rooted trees New Hampshire/Newick Tree Format Links: TreeView. Online Manual is here. Phylodendron Adventures of Baron Munchausen MacGSView
Session 6 (6/10)	Addendum to class #5 Maximum Likelihood Approaches: Testing trees and models using the ML ratio test Maximum likelihood mapping. Assignment #6 Links: TREE-PUZZLE Chi Square Calculator (for Windows) Chi Square Table
Session 7 (6/11)	Genome-wide Analyses. SEALS Demo. Assignment #7 Links: SEALS TaxPlot Taxonomy Browser
Session 8 (6/12)	Protein Structure Database: PDB Comparison and manipulation of 3D structures. Introduction to SPdbV. Assignments #8: Part I Part II Part III Part IV Links: CDD search PDB SPDBV. Tutorial is here. POV-RAY
Session 9 (6/13)	MrBayes by Example: Influenza Hemagglutinin protein evolution. Assignment #9. Links: MCRobot MrBayes
Session 10 (6/14)	Exam (2 hours) Comments? Suggestions? - Send Feedback Acknowledgments

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