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Syllabus (evolving to reflect what actually happens)

last updated 3/10/2004
Date
Lecture
Topics
Assignments:
Reading/Problem Sets
Jan 5, M Introduction
(Lowe, Rohl)
Administrative issues, background, goals, definitions Claverie, Ch 1
Gibbs, Ch 1,2
Jan 7, W Genomes and Genomics
(Lowe)
Genome sequenceing, genome databases, gene finding, annotating genomes, browsers Claverie Ch 2,3
Gibbs Ch 6
Jan 9, F Setting Up Laptops Installing X11, Cygwin, and other stuff for a Unix environment Claverie, Ch 4
Jan 12, M DNA Sequence Databases
(Lowe)
Sequence databases, formats Claverie, Ch 5
Gibbs, Ch 7, p159-171
Jan 14, W Protein Sequence Analysis
(Rohl)
protein sequence databases, calculating physical properties from sequence, finding sequence motifs/signals, secondary structure prediction Claverie, Ch 6
Jan 16, F Problem Set #1
(Lowe, Rohl)
Claverie Ch 14,15
Gibbs, Ch 4-5
Jan 19, M HOLIDAY (no class)
Jan 21,
W
Dynamic Programming
(Lowe)
Global and local alignment, gap penalties, evolutionary distance, repetitive sequences Claverie, Ch 8
Jan 23, F Review Problem Set #1B

Gibbs, Ch 12
Problem Set #1 due
Jan 26, M Problem Set #2
(Lowe)
Installing seqaln; Unix programs and commands
Jan 28, W BLAST
(Lowe)
Versions of BLAST, statistical significance Claverie, Ch 7
Gibbs, Ch 7, p172-188
Jan 30, F BLASTing Protein Sequences
(Rohl)
Protein similarity and homology; Profiles; PSSMs, PSIBLAST Problem Set #2 due
Feb 2, M Problem Set #3
(Lowe, Rohl)
Feb 4, W Remote Homology Detection
(Rohl)
Profile alignment, Hidden Markov Models, fold-recognition, SAM-T02
Feb 6, F Multiple Sequence Alignments
(Rohl)
Progressive and heirarchical methods (ClustalW, Tcoffee), editing alignments (Jalview), sequence logos Claverie, Ch 9
Feb 9, M Problem Set #4
(Rohl)
Claverie Ch 10 Problem Set #3 due
Feb 11, W Phylogeny & COGs (Lowe) Phylogenetic trees & tools; COGs Gibbs, Ch 8
Feb 13, F Phylogeny (cont)
(Lowe)
Building trees, maximum parsimony, maximum likelihood, neighbor joining, bootstrapping Claverie, Ch 13
Feb 16, M HOLIDAY (no class)
Feb 18, W Problem Set #5
(Lowe)
Problem Set #4 due
Feb 20, F Molecular Graphics (Rohl)

Guest Lecturer:
Bill Scott

Molecular graphics in PyMOL Claverie, Ch 11
Gibbs, Ch 9
Feb 23, M Problem Set #6
(Rohl)
Problem Set #5 due
Feb 25. W Protein Structures and Models
(Rohl)
Experimental structures, predicted structures, modeling tools, model accuracy, model validation Gibbs, Ch 10
Feb 27, F Protein Structure Anaylsis
(Rohl)
structure comparison structure classification, structure-based alignments (Dali, VAST, Profit),
Mar 1, M Problem Set #7
(Rohl)

Pymol Redux: The Return of Bill Scott

Mar 3, W Genome Analysis
(Lowe)
ORFs, splice sites, regulatory sites, repeat masker, synteny Problem Set #6 due
Gibbs, Ch 11
Mar 5, F Problem Set #7 lab time
Mar 8, M Review Problem Set #7 due
Claverie, Ch 14
Mar 10, W RNA Genomics
(Lowe)
Course Evaluations

tRNAs, snoRNAs, types of RNA gene features

Claverie, Ch 12
Mar 12, F Exam