| Home | Class
Calendar |
Resource Links | Problem Sets |
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Date
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Lecture
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Topics
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Lab / Class Exercises |
Reading
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Problem Sets |
| April 4, Tu |
Introduction |
Administrative issues, background, goals, overview of course |
Claverie Ch 1,14 |
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| Apr 6, Th |
Genome and
DNA Sequence Databases |
Genome databases, annotating genomes, sequence databases,
sequence formats, retreiving sequences from databases |
Explore NCBI Resources; Use UCSC & IMG Genome Browsers |
Claverie Ch 2 (pp.33-63), Ch 3 (pp.73-104,113-115) |
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| Apr 11, Tu | BLAST:
similarity-based database searches |
Demonstration of UCSC Browser BLAST algorithm, flavors of BLAST, statistical significance |
Claverie Ch 7,8 NCBI BLAST Guide |
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| Apr 13, Th | Two Sequence Alignment & Scoring
Schemes |
Dot plots, global and local
alignment, scoring schemes,
Smith-Waterman |
Using NCBI BLAST | |
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| Apr 18, Tu | Protein
Databases and
Single Sequence
Protein Analysis and BLASTP |
Physical properties of proteins; motifs, signals, and secondary structure | In-class PSI-BLAST |
Claverie Ch 4, 6 | Prob Set #1 Assigned |
| Apr 20, Th | Multiple Sequence Alignments | Progressive and heirarchical
methods,
editing alignments, sequence logos; Genome alignments |
In class: ClustalW, Jalview |
Claverie, Ch 9, 10 | |
| Apr 25, Tu | Basic DNA Sequence Analysis |
ORF & gene finding, restriction site analysis, primer
selection |
See problem set #2 for
in-class exercises |
Prob Set #1 Due |
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| Apr 27, Th | Basic DNA Sequence Analysis
(continued) |
Using the SDSC Biology Workbench
& the UCSC Genome Table Browser |
Prob Set #2 Assigned | ||
| May 2, Tu | Functional Genomics |
COGs, GO, Pathway databases Using the IMG Database at JGI |
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May 4, Th |
Putting it All Together |
Midterm Review |
Midterm practice problems | Prob Set#2 Due |
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| May 9, Tues |
RNA Genomics I | Basics: Types of RNA gene
features, predicting secondary
structure Specialized RNA Databases, RFAM |
Claverie Ch 12 | ||
| May 11, Th | Midterm | ||||
| May 16, Tu | Power outage -- no class |
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| May 18, Th | RNA Genomics II | RNA genefinders; RNA motif
searches; Distinguising between ncRNAs and protein coding regions |
Searching RFAM, mFOLD RNAz, Alifold |
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| May 23, Tu | Molecular Visualization (Bill Scott) |
Molecular graphics |
JMOL, Rasmol, PyMOL | Claverie Ch 11 |
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| May 25, Th | Introduction (Part 1) Protein Structures and Models (Part 2) (David Bernick) |
Experimental structures, predicted structures, modeling tools, model accuracy, model validation | Problem
Set#3 Assigned |
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| May 30, Tu | Protein
Structure Anaylsis (David Bernick) |
Structure comparison structure classification,
structure-based alignments Dali, VAST |
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| Jun 1, Th | Phylogenomics | Building trees, bootstrapping Gene family trees, ortholog/paralog discrimination |
Build your own trees |
Claverie Ch 13 |
Prob Set #3 Due Prob Set #4 Assigned |
| Jun 6, Tue |
Review | Review All Problem Sets |
Practice questions |
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| Jun 8, Th |
Guest speaker |
More practice questions Course Evaluations |
Prob Set #4 Due |