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BME 110 - Class Calendar

last updated 04/06/2011
Class Demos/Exercises
Problem Sets
Mar 29, Tu
Introduction / Where is Genomics Today?
Administrative issues, background, goals, overview of course

Dummies Ch 1,
Ch 2 (pp.29-56), Ch 14

No Discussion Section This Week

Mar 31, Th

Sequence & Genome Databases

Genome databases, annotating genomes, sequence databases, sequence formats, retrieving sequences from databases

Explore NCBI Resources

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.

Apr 5, Tu

BLAST: similarity-based database searches

BLAST algorithm, flavors of BLAST, statistical significance

DNA: NM_001436, Protein: NP_001427

NM_153631.2 (HOX3A)

Ch 7
Web-Based BLAST Tutorial

NCBI BLAST Program Selection Guide

Apr 4/6

Discussion Section

NCBI Databases & UCSC Genome Browsers

Using The Human UCSC Genome Browser: Tutorial (link fixed)

Using the Microbial/Archaeal UCSC Genome Browsers: Tutorial

Problem Set #1 Assigned
Apr 7, Th Two Sequence Alignment & Scoring Schemes

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

Ch 8

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

Apr 12, Tues

Basic DNA Sequence Analysis

ORF & gene finding, motif searches, using EMBOSS

Ch 5

Discussion Section

Apr 14, Th
Basic DNA Sequence Analysis (cont)

Apr 19, Tues
Protein Sequence Analysis and  Protein Databases

Physical properties of proteins; motifs, signals, and secondary structure
PFAM, ExPASy, InterPro
Using PFAM
Ch 4, 6

Discussion Section
Gene finding, Table Browser, Jalview
Discussion section problems
Install Jalview for/in Discussion Section

Apr 21, Th

Multiple sequence alignment

Progressive and heirarchical methods, editing alignments, sequence logos

ClustalW, Jalview, WebLogo

Ch 9, 10

Apr 26, Tues
Advanced Genome Browser Features

UCSC Table Browser

Fun Quiz #2

Pyrobaculum Genemark ORF prediction bed file

Problem Set #2 Assigned

Discussion Section
Practice problems for test & problem set

Apr 28, Th


Gene family trees, ortholog/paralog discrimination

Fun Quiz #3

Ch 13
PS#1 Key Posted
May 3, Tues
Phylogenomics (cont)

Review last year's Midterm
(key for midterm)
Please be sure to read Chapter 13 in Dummies on phylogenetic analysis carefully -- it has important material not discussed in class!

Discussion Section
Practice problems for problem set #2

May 5, Th

Midterm Review

Midterm Review
Tree building exercises

Fun Quiz #4

May 10, Tues



PS#2 Key Posted

Discussion Section

May 12, Th

RNA Genomics

Types of RNA gene features, Predicting RNA secondary structure

Distinguishing between ncRNAs and protein coding regions


Ch 12

May 17, Tu

RNA Genomics (cont)

RNA genefinders;
Specialized RNA Databases, RFAM

Searching RFAM
Example Ribosomal RNA tree for Archaea

Discussion Section

May 19, Th
Functional Genomics

COGs, GO, Pathway databases
Microarray & RNA-seq Data

Non-homology methods Review (Marcotte 2000)

Problem Set#3 posted

May 24, Tu
Protein Structures and Models
(Guest lecturer: John Archie)

Experimental structures, predicted structures, modeling tools, model accuracy, model validation Using PyMOL Ch 11

Song et al. paper

Discussion Section
Discussion Section Practice Problems

May 26, Th Protein Structure Analysis
(Guest lecturer: John Archie)

Structure comparison structure classification, structure-based alignments

May 31, Tue

Practice problems from previous final exam

Homology Review (Fitch 2000)

Discussion Section
Review Problem Sets

Jun 2, Th
Challenge Questions

Start to Finish: Sequencing, Assembly, Annotating, Creating a Genome Browser, & Publishing your Genome

Practice questions

Problem Set#3 Key Posted
Jun 8, Wed

Final Exam