Home Class Calendar
Resource Links Problem Sets

BME 110 - Class Calendar

last updated 4/04/2005
Problem Sets
Mar 29, Tu
(Lowe, Corey)
Administrative issues, background, goals, overview of course

Claverie Ch 1,14

Mar 31, Th
Genome and DNA Sequence Databases
Genome databases, annotating genomes, sequence databases, sequence formats Explore NCBI Resources, UCSC Genome Browsers
Claverie Ch 2,3

Prob Set #1 Assigned
Apr 5, Tu
Basic DNA Sequence Analysis
ORF prediction, Restriction site analysis, Primer design, Content analysis NEB tools, Primer3, ORF/gene finding, Biology Workbench
In-class exercise
Claverie, Ch 5

Apr 7, Th
Protein Sequence Analysis
Protein databases; physical properties of proteins; motifs, signals, and secondary structure Links from Lecture
Claverie Ch 4,6

Apr 12, Tu
Two sequence alignment
Dot plots, global and local alignment, scoring schemes, Smith-Waterman algorithm
In-class exercise
Claverie Ch 8

Prob Set #2 Assigned
Apr 14, Th
BLAST algorithm, flavors of BLAST, statistical significance, repeat masker
Claverie Ch 7

Prob Set #1 Due
Apr 19, Tu
BLASTing Protein Sequences
Protein similarity and homology; Profiles; PSSMs, PSI-BLAST Using PSSMs in BLAST, PSI-BLAST

Apr 21, Th
Remote Homology Detection
Profile alignment, Hidden Markov Models, fold-recognition
Using SAM-T02

Apr  26, Tu
Multiple Sequence Alignments
Progressive and heirarchical methods, editing alignments, sequence logos ClustalW, Tcoffee, Jalview, LOGO
Claverie, Ch 9, 10
Prob Set #2 Due
Prob Set #3 Assigned
Apr 28, Th
Phylogenentics: Building trees, maximum parsimony, maximum likelihood, neighbor joining, bootstrapping Midterm Review
Sample Questions from last year's final
Claverie Ch 13
May 3, Tu Midterm

May 5, Th Molecular Visualization
(Bill Scott)
Molecular graphics
JMOL, Rasmol, PyMOL Claverie Ch 11

May 10, Tu Protein Structures and Models
(David Bernick)
Experimental structures, predicted structures, modeling tools, model accuracy, model validation

May 12, Th Protein Structure Anaylsis
Structure comparison structure classification, structure-based alignments
Dali, VAST, Profit
Prob Set #3 Due
Prob Set #4 Assigned
May 17, Tu Functional Classification
COGs, Gene Ontology, Pathway Databases Exploring Pathway Databases - KEGG, BioCyc

May 19, Th RNA Genomics

Basics: Types of RNA gene features, predicting secondary structure
Specialized RNA Databases, RFAM

RFAM, RNAz, Alifold
Claverie Ch 12
May 24, Tu RNA Genomics II
Specific RNA genefinders

Prob Set #4 Due

May 26, Th Practical Phylogenetic Analysis
(Chad Saltikov)

Prob Set #5 Assigned
May 31, Tue
Final Review

Jun 2, Th
Final Review (cont.)

Prob Set #5 reviewed

Course Evaluations

Prob Set #5 Due