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BME 110 - Class Calendar

last updated 3/30/2010
Class Demos/Exercises
Problem Sets
Mar 30, Tu

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


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


Ch 7

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

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)


Gene family trees, ortholog/paralog discrimination

Ch 13
Problem Set #2 posted
May 4, Tues

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

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 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

Final Exam