|
Date
|
Lecture
|
Topics
|
Class Demos/Exercises |
Reading
|
Problem Sets |
| April 1, Tue |
Introduction |
Administrative issues, background, goals, overview of course Genome sequencing & databases |
Ch 1, 2 |
||
| Apr 3, Th |
Genome and
DNA Sequence Databases |
Genome databases, annotating genomes, sequence databases,
sequence formats, retrieving sequences from databases |
Explore NCBI Resources; Using UCSC Genome Browsers |
Prob Set #1 Assigned | |
| Apr 8, Tue | Two
Sequence Alignment &
Scoring
Schemes |
Dot plots |
Dotlet demo |
Ch 3 |
|
| Apr 10, Th | Two sequence alignment (cont) Protein Databases |
Global and local
alignment, scoring schemes,
Smith-Waterman Single protein sequence properties, SwissProt, UniProt, PDB |
Prob Set #1 Due Friday Apr 11, 5pm |
||
| Apr 15, Tue | BLAST: similarity-based database searches |
BLAST algorithm, flavors of BLAST, statistical significance |
Using NCBI BLAST Class / review section exercises |
Ch 6 NCBI BLAST Guide |
|
| Apr 17, Th |
BLAST (continued) |
BlastP, PSI-BLAST |
In-class WebCT quiz |
||
| Apr 22 Tues | Multiple Sequence Alignments |
Progressive and heirarchical
methods,
editing alignments, sequence logos; Pfam |
ClustalW, Jalview In-class exercise Study Section practice problems |
Ch 5 | |
| Apr 24, Thu | Phylogenomics |
Building trees, bootstrapping Gene family trees, ortholog/paralog discrimination |
In-class WebCT quiz Ribosomal RNA Sequence file More Jalview practice; TreeView |
Ch 7 |
|
| Apr 29, Tues | Phylogenomics (cont). |
||||
| May 1 Thu |
Bio
Tool Frameworks Guest Lecture: David Bernick |
SDSC Workbench; ExPasy Tools |
|||
| May 6, Tue | Single Sequence Analysis: DNA | Practice using NCBI ORF Finder; Primer3, NEB Restriction Enzyme searches | Prob Set #2 Posted |
||
| May 8, Th | Midterm |
Midterm review |
Review Last Year's Midterm Practice problems Study Guide for material from textbook |
Practice Problem Set#2 Answers posted |
|
| May 13, Tue |
Midterm |
||||
| May 15, Th | RNA
Genomics |
Types of RNA gene
features, Predicting RNA secondary
structure; Specialized RNA Databases, RFAM mfold; RNA genefinders |
Demo: Searching RFAM, mFOLD, tRNAscan-SE | Ch8 |
Prob Set #2 Due Prob Set#2 Answer key |
| May 20, Tue | RNA Genomics (cont) Functional Genomics |
COGs, GO, Pathway databases |
WebCT quiz on reading in Ch 8
& 9 |
Ch 11 |
Prob
Set #3 Assigned |
| May 22, Th |
Molecular Visualization (Bill Scott) |
Molecular graphics | JMOL, Rasmol, PyMOL | |
|
| May 27, Tue | Protein
Structures and Models (David Bernick) |
Experimental structures, predicted structures, modeling tools, model accuracy, model validation | Ch 10 |
Probl Set #3 Due Prob Set #4 Assigned |
|
| May 29, Th | Protein
Structure Anaylsis (David Bernick) |
Structure comparison structure
classification,
structure-based alignments Dali, VAST |
In class exercise files: 1SI2.pdb 1U04.pdb mol2_1-2.pdb VAST1u04Alignments.cn3 Supplemental Structure Information for Song et al., Science 2004. |
||
| Jun 3, Tue |
Bringing it All
Together: Genome Analysis |
WebCT practice questions |
Ch 11 (cont.) |
Prob Set #4 Due on Wednesday June 4th, at 11:55pm |
|
| Jun 5, Th |
Practice Questions | Review last year's final exam, any questions from problem Sets |
Practice questions: Last Year's Exam Part 1 Part 2 Course Evaluations Special Review Session scheduled for Friday, June 6th, Noon-2pm, PSB 305 |
Prob Set#1 Answer key Prob Set#2 Answer key Prob Set#3 Answer key Prob Set#4 Answer key Pymol saved sessions: Q2, Q3, Q4, Q6 |
|
| Jun 9, Mon |
Final Exam, 4-7pm |