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Date
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Lecture
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Topics
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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 |
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| 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 |
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| 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) |
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| 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: |
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 |
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| 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 |
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| Mar 10, W | RNA Genomics (Lowe) |
Course Evaluations
tRNAs, snoRNAs, types of RNA gene features |
Claverie, Ch 12 |
| Mar 12, F | Exam |