Applied Bioinformatics BIT150


Instructors:     Jorge Dubcovsky. (1st half )

David Neale. (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.