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BIO 5376/4375 (Fall 2005) Applied Bioinformatics

A graduate-level course that presents a practical approach to quantitative and statistical analysis of biological sequence and structural information. Classroom lectures are accompanied by practical demonstrations and laboratory exercises. Topics may include, but are not limited to, genomic information content, data searches and sequence alignment, mutations and distancebased phylogenetic analysis, genomics and gene recognition, polymorphisms and forensic applications, nucleic-acid and protein array analysis, structure prediction of biological macromolecules.


Two semesters calculus and one semester introductory statistics or BIOL 5V00-6A/6M and MATH 5V00-6A/6M TR 11:00 - 12:15 PM FO 3.616 (lecture) and TBA (lab) Stephen Levene FN 3.114 Phone: X2503, Email: TR 2-3 PM and by appointment Bioinformatics and Functional Genomics by Jonathan Pevsner Wiley-Liss, Hoboken, NJ; 2003 ISBN 0471210048 Other assigned or recommended readings, including journal articles, as appropriate. All students registered for this class are required to have computer and internet access. Student computer accounts can be obtained through UTD’s Information Resources department at no cost. In-class quizzes (50%); two 75-min exams (25% each). Ungraded homework assignments (and answers) will be distributed as a study aid. No makeup quizzes or exams will be given except in case of a serious emergency (documentation required). details, see Failure to comply with these terms will be subject to appropriate disciplinary action.




ACADEMIC DISHONESTY POLICY Students are required to abide by UT-Dallas policies concerning academic integrity (for


If you wish to submit an examination or quiz question for regrading, my policy is that the entire exam or quiz then becomes eligible for regrading. If there are erroneous answers that I missed previously, regrading may cause your exam or quiz score to decrease instead of increase. If you have a disability that requires accommodation, you must notify the instructor and file a request through Disability Services (SU 1.610, x2098) on or before the first day of class. By doing so, you can be assured of full cooperation in making appropriate arrangements.


Week 1 2 3



Date 8/18

Topic Overview and Introduction Accessing biological databases Quiz, BLAST searches (Dr. Bu) Lab: BLAST searching Quiz, Simulation of biological macromolecules Lab: Protein-structure visualization tools Exam No. 1 (covers all material up to 9/22) Molecular phylogeny and trees (cont’d) Quiz, Multiple alignment (cont’d) Lab: Genome databases Quiz, Genetic disorders Protein and nucleic-acid arrays (cont’d) Quiz, Lab: Microarray analysis Using Matlab’s Bioinformatics Toolbox

Assigned Readings
Ch. 1 Ch. 2,3 Chs. 3,4

8/23 8/30

Sequences and strings Pairwise alignment, dynamic programming (Dr. Bu) Advanced BLAST methods (Dr. Pace) The protein-folding problem Protein-structure prediction Protein-structure prediction (cont’d) Molecular phylogeny and trees Multiple alignment Genomic analysis SNPs, forensic applications Protein and nucleic-acid arrays Using Matlab’s Bioinformatics Toolbox Using Matlab’s Bioinformatics Toolbox Exam No. 2

8/25 9/1

4 5

9/6 9/13

9/8 9/15

Chs. 4,5 Chs. 8,9

6 7 8 9 10 11 12 13 14 15

9/20 9/27 10/4 10/11 10/18 10/25 11/1 11/8 11/15 11/22

9/22 9/29 10/6 10/13 10/20 10/27 11/3 11/10 11/17

Ch. 9 TBA Ch. 10 Ch. 11 Chs. 12,14,15 Chs. 16, 17 Ch. 18 Ch. 7 TBA