Bioinformatics: Programming
Long Title: Bioinformatics: Programming
Short Title: Bio Info Prog
ZOO 5913 3 hour
MW 10:30 - 11:45 NH122 (Nielsen Hall computer lab)
http://www.ou.edu/cas/zoology/Courses/BioInfoProg.htm
Tom Ray, 325-3526, tray@ou.edu, Sutton Hall Room 210
Prerequisites: ZOO5905 "Bioinformatics: Applications", and C or C++ programming ability (CS2413 Data Structures, or MIS3013 C Programming) and permission of instructor.
The course is designed to provide programming skills needed
to perform large-scale genomic analysis in research and professional settings. The Perl programming language will
be taught by introducing features of the Perl programming language in the context of and with applications to
bioinformatics. Libraries of Perl code modules with applications to bioinformatics, such as BioPerl and the
NCBI Toolkit, will be introduced. These modules can be used for accessing sequence data from local and remote
databases, transforming formats of database/file records, manipulating individual sequences, searching for "similar"
sequences, creating and manipulating sequence alignments, searching for genes and other structures on genomic DNA,
and developing machine readable sequence annotations.
Required Textbooks:
"Beginning Perl for Bioinformatics" by James D. Tisdall
Paperback: 400 pages; 1st edition (October 15, 2001)
O'Reilly & Associates; ISBN: 0596000804;
"Perl Cookbook" by Tom Christiansen, Nathan Torkington, Larry Wall
Paperback: 794 pages; (August 1998)
O'Reilly & Associates; ISBN: 1565922433;
"Perl Pocket Reference", 4th Edition by Johan Vromans
Paperback: 96 pages; 4th edition (July 2002)
O'Reilly & Associates; ISBN: 0596003749;
Recommended Textbooks:
"Learning Perl", Third Edition by Randal L. Schwartz, Tom Phoenix
Paperback: 316 pages; 3rd edition (July 15, 2001)
Publisher: O'Reilly & Associates; ISBN: 0596001320;
Programming Perl (3rd Edition)
by Larry Wall, Tom Christiansen, Jon Orwant
Paperback: 1092 pages; 3rd edition (July 2000)
Publisher: O'Reilly & Associates; ISBN: 0596000278;