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BME 110 - Class Calendar

last updated 04/06/2011
Date
Lecture
Topics
Class Demos/Exercises
Reading
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
Fun with BLAST & EMBOSS



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
PSI-BLAST,
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
Galaxy



Fun Quiz #2

Pyrobaculum Genemark ORF prediction bed file


Problem Set #2 Assigned

Discussion Section
Practice problems for test & problem set




Apr 28, Th

Phylogenomics

Gene family trees, ortholog/paralog discrimination

Fun Quiz #3

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



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

Midterm



 


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

RNAfold

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
Review

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
12-3pm

Final Exam