| Home | Class
Calendar |
Resource Links | Problem Sets |
|
Date
|
Lecture
|
Topics
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Class Demos/Exercises |
Reading
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Problem Sets |
| Mar 31, Tu |
Introduction Genome Databases |
Administrative issues, background, goals, overview of course Genome databases, annotating genomes, sequence databases, sequence formats, retrieving sequences from databases |
Ch 1, Ch 2 (pp.29-56) |
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| Apr 2, Th |
Sequencing Technology, DNA Sequence Databases |
NCBI, UCSC Genome Browsers |
Explore NCBI Resources; Using UCSC & IMG Genome Browsers In-class exercises |
Dummies: Ch 3 Assigned Review: "The impact of next-generation sequencing technology on genetics" by E. Mardis Recommended Review: "Application of ‘next-generation’ sequencing technologies to microbial genetics" by MacLean et al. |
|
| Apr 7, Tu | Genome and DNA Sequence
Databases (cont.) |
Finshing in-class demonstrations
for Sequence Databases & Genome databases |
Prob Set #1 Assigned | ||
| Apr 9, Th | BLAST: similarity-based database searches |
BLAST algorithm, flavors of BLAST, statistical significance |
Using NCBI BLAST |
Ch 7 NCBI BLAST Guide |
Last Year's Problem Set#1 Key |
| Apr 14, Tues | BLAST (cont) |
More BLAST Practice |
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| Apr 16, Th | Two Sequence Alignment & Scoring Schemes |
Dot plots, global and local
alignment, scoring schemes,
Smith-Waterman |
Ch 8 Practice problems from last year and Answer key |
Prob Set #1 Due Today (thurs),
10am |
|
| Apr 21, Tues | Basic
DNA Sequence Analysis |
ORF & gene finding, restriction site analysis, primer
selection |
Example
sequences |
Ch 5 |
Prob Set #2 Assigned |
| Apr 23, Th | Basic DNA Sequence Analysis (cont) |
Using Artemis |
Practice using Artemis, Primer3, NEB Restriction Enzyme searches |
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| Apr 28, Tues | Multiple
Sequence Alignment |
Progressive and heirarchical
methods,
editing alignments, sequence logos; Genome alignments |
ClustalW, Jalview, TreeView Sequences for In-class exercises |
Ch 9, 10 | Prob Set #1 Key posted |
Apr 30, Th |
Multiple Sequence Alignment (cont) |
Midterm from last year & objectives |
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Prob Set#2 Due |
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| May 5, Tues |
Phylogenomics Review |
Building trees, bootstrapping Gene family trees, ortholog/paralog discrimination Midterm, Problem Set Review |
Reverse
gyrase example seqs |
Prob Set #2 Key posted |
|
| May 7, Th | Midterm |
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| May 12, Tues | Protein
Sequence Analysis and Protein Databases / Functional Genomics (David Bernick) |
Physical properties of proteins;
motifs,
signals, and secondary structure PFAM, ExPASy tools COGs, GO, Pathway databases |
PSI-BLAST, Using PFAM |
Ch 4, 6 Ch 13 |
|
| May 14, Th | RNA Genomics |
Types of RNA gene
features, Predicting RNA secondary
structure; Distinguising between ncRNAs and protein coding regions |
Demo: Searching RFAM, mFOLD | Ch 12 |
|
| May 19, Tu | RNA Genomics (cont) |
mfold; RNA genefinders; Specialized RNA Databases, RFAM |
Prob Set #3 Assigned | ||
| May 21, Th | Protein Structures and Models (David Bernick) |
Experimental structures, predicted structures, modeling tools, model accuracy, model validation | Using PyMOL Download Structures |
Ch 11 Song et al. paper |
|
| May 26, Tu | Protein Structure Analysis (Martina Koeva) |
Structure comparison structure
classification,
structure-based alignments Dali, VAST |
|
Prob Set#3 Due Wednesday, May 27 11pm Problem Set #4 Assigned |
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| May 28, Th | Protein
Structure Prediction (Kevin Karplus) |
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| Jun 2, Tue |
Review |
|
Final exam 2008 Part 1 Final exam 2008 Part 2 |
Prob Set #3 Key |
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| Jun 4, Th |
Challenge Questions | Review All Problem Sets |
Practice questions Course Evaluations |
Problem Set #4 Due 10am in class | |
| Jun 9, Tu 7:30pm |
Final Exam |