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BME 110 - Class Calendar

last updated 4/11/2006
Lab / Class Exercises
Problem Sets
April 4, Tu

Administrative issues, background, goals, overview of course

Claverie Ch 1,14

Apr 6, Th
Genome and DNA Sequence Databases

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

Claverie Ch 2 (pp.33-63), Ch 3 (pp.73-104,113-115)

Apr 11, Tu BLAST: similarity-based database searches
Demonstration of UCSC Browser
BLAST algorithm, flavors of BLAST, statistical significance

Claverie Ch 7,8

Apr 13, Th Two Sequence Alignment & Scoring Schemes

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


Apr 18, Tu Protein Databases and Single Sequence Protein Analysis and BLASTP
Physical properties of proteins; motifs, signals, and secondary structure In-class PSI-BLAST
Claverie Ch 4, 6 Prob Set #1 Assigned
Apr 20, Th Multiple Sequence Alignments Progressive and heirarchical methods, editing alignments, sequence logos;  Genome alignments
In class: ClustalW, Jalview
Claverie, Ch 9, 10
Apr 25, Tu Basic DNA Sequence Analysis

ORF & gene finding, restriction site analysis, primer selection
See problem set #2 for in-class exercises

Prob Set #1 Due

Apr 27, Th Basic DNA Sequence Analysis (continued)
Using the SDSC Biology Workbench & the UCSC Genome Table Browser

Prob Set #2 Assigned
May 2, Tu Functional Genomics
COGs, GO, Pathway databases
Using the IMG Database at JGI

May 4, Th

Putting it All Together

Midterm Review
Midterm practice problems

Prob Set#2 Due

May 9, Tues
RNA Genomics I Basics: Types of RNA gene features, predicting secondary structure
Specialized RNA Databases, RFAM

Claverie Ch 12

May 11, Th Midterm

May 16, Tu Power outage -- no class

May 18, Th RNA Genomics II RNA genefinders; RNA motif searches; Distinguising between ncRNAs and protein coding regions
Searching RFAM, mFOLD
RNAz, Alifold

May 23, Tu Molecular Visualization
(Bill Scott)
Molecular graphics
JMOL, Rasmol, PyMOL Claverie Ch 11

May 25, Th Introduction (Part 1)
Protein Structures and Models
(Part 2)
(David Bernick)
Experimental structures, predicted structures, modeling tools, model accuracy, model validation

Problem Set#3 Assigned

May 30, Tu Protein Structure Anaylsis
(David Bernick)

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

Jun 1, Th Phylogenomics Building trees, bootstrapping
Gene family trees, ortholog/paralog discrimination
Build your own trees

Claverie Ch 13
Prob Set #3 Due Prob Set #4 Assigned
Jun 6, Tue
Review All Problem Sets

Practice questions

Jun 8, Th
Guest speaker

More practice questions
Course Evaluations

Prob Set #4 Due