| Home | Class
Calendar |
Resource Links | Problem Sets |
|
Date
|
Lecture
|
Topics
|
Lab |
Reading
|
Problem Sets |
| Mar 29, Tu |
Introduction (Lowe, Corey) |
Administrative issues, background, goals, overview of course |
Claverie Ch 1,14 |
||
| Mar 31, Th |
Genome and
DNA Sequence Databases (Lowe) |
Genome databases, annotating genomes, sequence databases, sequence formats | Explore NCBI Resources, UCSC
Genome Browsers |
Claverie Ch 2,3 |
Prob Set #1 Assigned |
| Apr 5, Tu |
Basic DNA Sequence
Analysis (Lowe) |
ORF prediction, Restriction site analysis, Primer design, Content analysis | NEB tools, Primer3, ORF/gene
finding, Biology Workbench In-class exercise |
Claverie, Ch 5 |
|
| Apr 7, Th |
Protein
Sequence Analysis (Corey) |
Protein databases; physical properties of proteins; motifs, signals, and secondary structure | Links from Lecture |
Claverie Ch 4,6 |
|
| Apr 12, Tu |
Two sequence
alignment (Lowe) |
Dot plots, global and local alignment, scoring schemes,
Smith-Waterman algorithm |
In-class exercise |
Claverie Ch 8 |
Prob Set #2 Assigned |
| Apr 14, Th |
BLAST (Lowe) |
BLAST algorithm, flavors of BLAST, statistical significance,
repeat masker |
Using NCBI BLAST |
Claverie Ch 7 NCBI BLAST Guide |
Prob Set #1 Due |
| Apr 19, Tu |
BLASTing
Protein Sequences (Corey) |
Protein similarity and homology; Profiles; PSSMs, PSI-BLAST | Using PSSMs in BLAST,
PSI-BLAST |
||
| Apr 21, Th |
Remote
Homology Detection (Corey) |
Profile alignment, Hidden Markov Models, fold-recognition |
Using SAM-T02 |
|
|
| Apr 26, Tu |
Multiple
Sequence Alignments (Corey) |
Progressive and heirarchical methods, editing alignments, sequence logos | ClustalW, Tcoffee, Jalview,
LOGO |
Claverie, Ch 9, 10 |
Prob Set #2 Due Prob Set #3 Assigned |
| Apr 28, Th |
Phylogeny (Corey) |
Phylogenentics: Building trees, maximum parsimony, maximum likelihood, neighbor joining, bootstrapping | Midterm Review Sample Questions from last year's final |
Claverie Ch 13 | |
| May 3, Tu | Midterm |
|
|||
| May 5, Th | Molecular Visualization (Bill Scott) |
Molecular graphics |
JMOL, Rasmol, PyMOL | Claverie Ch 11 |
|
| May 10, Tu | Protein
Structures and Models (David Bernick) |
Experimental structures, predicted structures, modeling tools, model accuracy, model validation | |||
| May 12, Th | Protein
Structure Anaylsis (Corey) |
Structure comparison structure classification,
structure-based alignments |
Dali, VAST, Profit | |
Prob Set #3 Due Prob Set #4 Assigned |
| May 17, Tu | Functional
Classification (Corey) |
COGs, Gene Ontology, Pathway Databases | Exploring Pathway Databases - KEGG, BioCyc | ||
| May 19, Th | RNA Genomics (Lowe) |
Basics: Types of RNA gene features, predicting secondary
structure |
RFAM, RNAz, Alifold |
Claverie Ch 12 | |
| May 24, Tu | RNA Genomics II (Lowe) |
Specific RNA genefinders |
Prob Set #4 Due |
||
| May 26, Th | Practical
Phylogenetic Analysis (Chad Saltikov) |
|
Prob Set #5 Assigned | ||
| May 31, Tue |
Final Review | |
|
||
| Jun 2, Th |
Final Review (cont.) |
Prob Set #5
reviewed Course Evaluations |
Prob Set #5 Due |