ZOO 5903 Sect 001 Bioinformatics: Applications, 3 hour
MW 10:30 - 11:45 NH122 (Nielsen Hall computer lab)
Tom Ray, 325-3526, 203-0703, Sutton Hall Room 210
http://www.ou.edu/cas/zoology/bioinformatics_course.htm
I. Introduction to Bioinformatics
1 Aug 22 M Lecture - Introduction
II. Unix Basics
2 Aug 24 W Lecture - Linux
3 Aug 29 M Lab - Linux
III. Genome Sequencing and Databases
4 Aug 31 W Lecture - Genome Sequencing, Phred, Phrap,
Consed, Sequin
5 Sep 7 W Lecture - guest lecture: Jim White &
Steve Kenton
6 Sep 12 M Lab - ACGT Tour
7 Sep 14 W Lecture - Assembly Process - The NCBI Data Model
8 Sep 19 M Lab - Data bases on the web
9 Sep 21 W Assisted Review
10 Sep 26 M Exam - Linux, Phred, Phrap, Consed, Sequin, Databases
IV. Sequence Alignment
11 Sep 28 W Lecture - Pairwise Alignment
12 Oct 3 M Lab - Dotter, Align, Lalign
13 Oct 5 W Lecture - Multiple Sequence Alignment
14 Oct 10 M Lab - CLUSTAL, MEME
V. Database Searching for Similar Sequences
15 Oct 12 W Lecture - Searching Databases to Match Sequences
16 Oct 17 M Lab - FASTA, BLAST, SSEARCH,
17 Oct 19 W Assisted Review
18 Oct 24 M Exam - Dotter, Align, Clustal, Meme, Fasta, Ssearch,
Blast
19 Oct 26 W Lecture - Searching Databases to Match Patterns
VI. Gene Analysis
20 Oct 31 M Lab - HMMER, MAST, PSI-BLAST
21 Nov 2 W Lecture - Gene Prediction
22 Nov 7 M Lab - Sim4, Genscan, GrailExp
23 Nov 9 W Exam - HMMER, MAST, PSI-BLAST - Sim4, Genscan,
GrailExp
VII. Protein Analysis
24 Nov 14 M Lecture - Predicting Protein Structure - PREDATOR
25 Nov 16 w Lecture - Protein Structure - CN3D, MMDB, VAST
26 Nov 21 M Lecture - Microarrays - guest lecture: Tyrrell Conway
VIII. Phylogenetic Prediction
27 Nov 28 M Lecture - Phylogenetic Prediction - Phylip
28 Nov 30 W Exam - CN3D, MMDB, VAST, PREDATOR, Phylip
29 Dec 5 M Lecture - Paup - guest lecture: Richard Broughton
IX. Introduction to Bioinformatics Programming
30 Dec 7 W Lecture - Perl in Bioinformatics
IMPORTANT: This syllabus is tentative. There will be changes.