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BME 110 - Class Calendar

last updated 4/20/2009
Date
Lecture
Topics
Class Demos/Exercises
Reading
Problem Sets
Mar 31, Tu
Introduction

Genome Databases

Administrative issues, background, goals, overview of course

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

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


Apr 2, 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.




Apr 7, Tu Genome and DNA Sequence Databases (cont.)
Finshing in-class demonstrations for Sequence Databases & Genome databases




Prob Set #1 Assigned
Apr 9, Th
BLAST: similarity-based database searches


BLAST algorithm, flavors of BLAST, statistical significance

Using NCBI BLAST

Ch 7
NCBI BLAST Guide



Last Year's Problem Set#1 Key
Apr 14, Tues
BLAST (cont)



More BLAST Practice







Apr 16, Th
Two Sequence Alignment & Scoring Schemes
Dot plots, global and local alignment, scoring schemes, Smith-Waterman


Ch 8

Practice problems from last year
and Answer key

Prob Set #1 Due Today (thurs), 10am


Apr 21, Tues Basic DNA Sequence Analysis

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


Prob Set #2 Assigned

Apr 23, Th
Basic DNA Sequence Analysis (cont)

Using Artemis



Practice using Artemis, Primer3, NEB Restriction Enzyme searches


Apr 28, Tues Multiple Sequence Alignment
Progressive and heirarchical methods, editing alignments, sequence logos;  Genome alignments



ClustalW, Jalview, TreeView
Sequences for In-class exercises

Ch 9, 10
Prob Set #1 Key
posted



Apr 30, Th

Multiple Sequence Alignment (cont)




Midterm from last year & objectives


Prob Set#2 Due

May 5, Tues
Phylogenomics

Review
Building trees, bootstrapping
Gene family trees, ortholog/paralog discrimination

Midterm, Problem Set Review
Reverse gyrase example seqs


Prob Set #2 Key posted
May 7, Th
Midterm






May 12, Tues Protein Sequence Analysis and  Protein Databases /
Functional Genomics

(David Bernick)

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

COGs, GO, Pathway databases

PSI-BLAST,
Using PFAM
Ch 4, 6


Ch 13

May 14, Th
RNA Genomics

Types of RNA gene features, Predicting RNA secondary structure;


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

Ch 12



May 19, Tu
RNA Genomics (cont)

mfold; RNA genefinders;
Specialized RNA Databases, RFAM



Prob Set #3 Assigned
May 21, Th
Protein Structures and Models
(David Bernick)

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

Download Structures
Ch 11

Song et al. paper

May 26, Tu
Protein Structure Analysis
(Martina Koeva)


Structure comparison structure classification, structure-based alignments
Dali, VAST


Prob Set#3
Due Wednesday, May 27 11pm

Problem Set #4
Assigned

May 28, Th Protein Structure Prediction
(Kevin Karplus)








Jun 2, Tue
Review






Final exam 2008 Part 1
Final exam 2008 Part 2

Prob Set #3 Key

Jun 4, Th
Challenge Questions
Review All Problem Sets

Practice questions
Course Evaluations


Problem Set #4 Due 10am in class
Jun 9, Tu
7:30pm

Final Exam