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BME 110 - Class Calendar

last updated 3/30/2010
Date
Lecture
Topics
Class Demos/Exercises
Reading
Problem Sets
Mar 30, Tu
Introduction

Genome Databases

Administrative issues, background, goals, overview of course

Genome databases, annotating genomes, sequence databases, sequence formats, retrieving sequences from databases
Lab Section Exercises
Dummies Ch 1,
Ch 2 (pp.29-56),
Ch 14


Apr 1, Th

Sequencing Technology,
DNA Sequence Databases

NCBI, UCSC Genome Browsers
Explore NCBI Resources;
Using UCSC & IMG Genome Browsers

BLAT

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.


Current Events:
"Disease Cause is Pinpointed with Genome" by Nicholas Wade, NY Times 3/10/2010


Apr 6, Tu Using UCSC Genome Browsers

In-class exercises


Genome Browser Tutorial


Prob Set #1 Assigned
Apr 6, Tue
Discussion Section
Genome Browsers

Practice problem set #1 (last year's homework)

Apr 8, Th BLAST: similarity-based database searches BLAST algorithm, flavors of BLAST, statistical significance

NCBI BLAST Tutorial

Ch 7
NCBI BLAST Guide





Apr 13, Tues
Two Sequence Alignment & Scoring Schemes


Dot plots, global and local alignment, scoring schemes, Smith-Waterman





Ch 8

Prob Set #1 Due Tuesday April 13, 5pm

Apr 13
Discussion Section
Fun with BLAST and Dotlet

Practice Problems for PS #2

Apr 15, Th Basic DNA Sequence Analysis

ORF & gene finding, restriction site analysis, primer selection
Ch 5



Apr 20, Tues Basic DNA Sequence Analysis (cont)

Using Gene Annotation Tools
Practice Primer3, NEB Restriction Enzyme searches





Apr 22, Th Protein Sequence Analysis and  Protein Databases
(Kevin Karplus)


Physical properties of proteins; motifs, signals, and secondary structure
PFAM, ExPASy tools


PSI-BLAST,
Using PFAM

Ch 4, 6


Apr 27, Tues Multiple sequence Alignment
Progressive and heirarchical methods, editing alignments, sequence logos


ClustalW, Jalview, WebLogo
Rpp29 seqs
More sample sequences
Ch 9, 10


Discussion Section


ORF prediciton, EMBOSS, Jalview, and WebLogo exercise


Practice problems


Apr 29, Th
Multiple Sequence Alignment (cont)

Phylogenomics



Gene family trees, ortholog/paralog discrimination


Ch 13
Problem Set #2 posted
May 4, Tues
Review

Distribute last year's midterm




May 4
Discussion Section
Review last year's midterm, do practice problems




May 6, Th
Functional Genomics

Midterm Topics Review

COGs, GO, Pathway databases

More Practice problems

Review on scoring matrices:

"Where did the BLOSUM62 alignment score matrix come from?" by S.R. Eddy


Problem Set#2 due at 6pm
May 6

Special Review Discussion section

Review problem set answers




Prob Set Answer Keys Posted
May 11, Tues
Midterm











May 13, Th
RNA Genomics


Types of RNA gene features, Predicting RNA secondary structure;

Distinguishing between ncRNAs and protein coding regions
Demo: Searching RFAM, mFOLD

Ch 12

Problem Set#3 posted

May 18, Tu
RNA Genomics (cont)

mfold; RNA genefinders;
Specialized RNA Databases, RFAM


Example Ribosomal RNA tree for Archaea




May 20, Th
Protein Structures and Models
(David Bernick)

Experimental structures, predicted structures, modeling tools, model accuracy, model validation Using PyMOL

Sequences for exercises

Ch 11

Song et al. paper



May 25, Tu
Protein Structure Analysis
(David Bernick)
Structure comparison structure classification, structure-based alignments
Dali, VAST


Problem Set #3 due Wednesday 6pm

Problem Set #4 Assigned
May 27, Th
Putting it all Together


Practice problems from previous final exam
Course Evaluations
Final Exam from 2009




Jun 1, Tue
Review

Review Problem Sets 1-3





Jun 2, Wed




Problem Set #4 Due, Wed 6pm

Jun 3, Th
Challenge Questions
(John St. John,
David Bernck)

Review Problem Set #4


Practice questions




Prob Set Answer Keys Posted
Jun 8, Tuesday
8-11am

Final Exam