BME 110 - Class Calendar

last updated 4/22/2008
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