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BME 110 - Class Calendar

last updated 3/13/2007
Date
Lecture
Topics
Class Demos/Exercises
Reading
Problem Sets
April 3, Tu
Introduction

Administrative issues, background, goals, overview of course

Ch 1,14


Apr 5, Th
Genome and DNA Sequence Databases

Genome databases, annotating genomes, sequence databases, sequence formats, retrieving sequences from databases
Explore NCBI Resources;
Using UCSC & IMG Genome Browsers

Ch 2 (pp.29-56), Ch 3


Apr 10, Tu Genome and DNA Sequence Databases (cont.)
Finshing in-class demonstrations for Sequence Databases & Genome databases




Prob Set #1 Assigned
Apr 12, Th
BLAST: similarity-based database searches




BLAST algorithm, flavors of BLAST, statistical significance



Using NCBI BLAST

Ch 7
NCBI BLAST Guide




Apr 17, Tues Blast (cont.)

Two Sequence Alignment & Scoring Schemes


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



More BLAST Practice



Ch 8

Prob Set #1 Due
Apr 19, Th Protein Sequence Analysis and  Protein Databases Physical properties of proteins; motifs, signals, and secondary structure
PFAM
PSI-BLAST,
Using PFAM
Ch 4, 6

Apr 24, Tues Basic DNA Sequence Analysis

ORF & gene finding, restriction site analysis, primer selection
In-class exercises
Ch 5


Prob Set #2 Assigned

Apr 26, Th
Basic DNA & Protein Sequence Analysis II

Using EMBOSS, ExPASy tools



Practice using Primer3, NEB Restriction Enzyme searches, EMBOSS, and ExPASy Tools



May 1, Tues Multiple Sequence Alignments Progressive and heirarchical methods, editing alignments, sequence logos;  Genome alignments ClustalW, Jalview
In-class exercise sequences

Ch 9, 10

May 3, Th

RNA Genomics I

Types of RNA gene features, Predicting RNA secondary structure; Specialized RNA Databases, RFAM,


Demo: Searching RFAM, mFOLD
Midterm practice problems & objectives

Ch 12
Prob Set#2 Due Friday May 4th 5pm



May 8, Tues
Review
Midterm review




May 10, Th
Midterm






May 15, Tues
RNA Genomics II
mfold; RNA genefinders;
Distinguising between ncRNAs and protein coding regions



May 17, Th Functional Genomics
Phylogenomics
COGs, GO, Pathway databases
Building trees, bootstrapping
Gene family trees, ortholog/paralog discrimination
Jalview, TreeView Ch 13 Prob Set #3 Assigned

May 22, Tu Molecular Visualization
(Bill Scott)
Molecular graphics JMOL, Rasmol, PyMOL Ch 11
May 24, Th
Protein Structures and Models
(David Bernick)
Experimental structures, predicted structures, modeling tools, model accuracy, model validation





May 29, Tu Protein Structure Anaylsis
(David Bernick)
Structure comparison structure classification, structure-based alignments
Dali, VAST
In class exercise files:
1SI2.pdb  1U04.pdb  mol2_1-2.pdb
VAST1u04Alignments.cn3
Supplemental Structure Information for Song et al., Science 2004.


Prob Set #3 Due Wed May 30 11:55pm

Prob Set #4 Assigned
May 31, Th Putting it all Together: Annotating Genomes IMG Database at JGI
UCSC Genome Table Browser
Making Custom Tracks for UCSC Genome Browsers



Jun 5, Tue
Integrating Tools to Solve Biological Problems

Answering non-trivial biological questions





Prob Set #4 Due
Wed June 6, 11:55pm
Jun 7, Th
Challenge Questions
Review All Problem Sets

Practice questions
Course Evaluations