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)

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Acknowledgments

The page is edited and maintained by Olga Zhaxybayeva
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Last modified on June 14 2002 09:22:52 AM