Monday/Wednesday/Friday 8th period (3:00 - 3:50 PM)
Office hour:
Monday/Wednesday 2:00-2:50 PM
Contact:
E436 (office), 392-6849 (office phone)
TA:
TBA
Goals:
This course will discuss the major components of
bioinformatics data (such as DNA and protein sequences and protein
structures) and how computer technology is used to understand this
data better.
Reading assignment: Shindyalov IN, Bourne PE (1998) Protein
structure alignment by incremental combinatorial extension (CE)
of the optimal path. Protein Engineering 11(9) 739-747.
(11/14/07)(new)
Reading assignment: Murzin A. G., Brenner S. E., Hubbard T.,
Chothia C. (1995). SCOP: a structural classification of proteins
database for the investigation of sequences and
structures. J. Mol. Biol. 247, 536-540. (11/14/07)(new)
Reading assignment: Protein structure comparison using
iterated double dynamic programming, WR Taylor, Protein Science,
Vol 8, Issue 3 654-665, 1999. (11/14/07)(new)
Check the class page regularly for announcements (06/12/07)
Prerequisites:
I will assume that you have already taken
data structures and algorithms courses and you are comfortable
with basic computer programming (e.g., with C or Java).
Topics:
I am planning to cover the following
topics.
Biological sequences
Lossless alignments (different DP problems such as global,
local alignment, etc,)
Lossy alignments (BLAST, etc)
Substitution matrices, statistics
Multiple alignment
Shotgun sequencing
Phylogeny
Protein structures and function (primary, secondary, etc.)
Structure alignment
Structure prediction
Pathways
Grading:
Grading will be based on homeworks (35 %),
project (50 %), and survey (15 %). I will reward high quality
projects with up to 2.5 % bonus points.
Text book:
I will teach this course from multiple books
and some research papers. Therefore, I do not require any
textbook. The primary book I will stick to is:
Fundamental Concepts of Bioinformatics by Dan E. Krane,
Michael L. Raymer. (ISBN: 0805346333)
For interested students, I recommend the following books as further resources.
Bioinformatics: Sequence and Genome Analysis by David
W. Mount. (ISBN: 0879696087)
Algorithms on Strings, Trees, and Sequences: Computer
Science and Computational Biology by Dan Gusfield. (ISBN:
0521585198)
Introduction to Protein Structure by Carl-Ivar Branden, John
Tooze.(ISBN: 0815323050)
Cheating, plagiarism, and other types of academic
dishonesty will be subject to punishment.
I encourage class attendence.
Please return your homeworks, project and surveys in
time. Late returns will cause 20 % deduction in your grade for
that homework (etc) for each late day.
Please visit only during office hours. If you really need to
meet me out of the office hours email me to make an
appointment. If I postpone or cancel the office hour, I will post
it in the announcements section and (try to) put a note on my
office door.
Please avoid any activities that will disturb the flow of
the lectures: Silence your cell phones, pagers, etc.
