Applied Bioinformatics BIT150
Instructors: Jorge Dubcovsky. firstname.lastname@example.org (1st half )
David Neale. email@example.com (2nd half )
The sequencing of hundreds of complete genomes has changed the way we work in biology. Today, most experiments start with detailed sequence analyses using powerful bioinformatics tools. A basic knowledge of these tools is essential to any job in the biotechnology industry today.
Learn how to:
· Analyze chromatograms
· Compare DNA and protein sequences
· Search efficiently for related sequences in DNA and protein databases
· Make multiple alignments
· Cluster multiple sequences & make evolutionary inferences
· Assemble sequences from thousands of chromatograms
· Annotate genes and repetitive regions
· Compare genomes
· Work with Express Sequence Tags (ESTs)
· Construct molecular maps and analyze QTLs
· Analyze allelic diversity and linkage disequilibrium
This class does not include programming or computer
languages. It is focused on the tools used to solve the problems described
above, the underlying biological concepts, and the correct interpretation and
application of their results. During the laboratory sections we will learn to
use different bioinformatics tools and programs including Chromas,
GeneTool, Sequin, Blast, ClustalW,
Mega4, T-coffee,Gap4, Gene prediction programs, Dotter, Phred/Phrap/Consed, etc. We will work
mainly with free web applications and LINUX applications in the UNIX Plant
Sciences server. The laboratory section will also include the discussion of
weekly bioinformatics problem series.
Grading: Letter grade will be based on the homework problem sets (40%), a mid-term examination (30%) and a final examination (30%).
Book: Bioinformatics. A
practical guide to the analysis of genes and proteins. A.D. Baxevanis & B.F.F. Ouellette.
Wiley-Interscience. Third Edition. 2005.