Program

The program provides a specific introduction to using genomic data in a biomedical laboratory. We split the course into morning sessions which introduce a topic with very applied and specific examples, highlighting just enough of the theory behind the tools to understand what's going on and how to choose parameters wisely. After the morning break, we will feature a lab scientist from our PGA or a collaborator to illustrate the use of genomics tools.

After lunch we will reconvene for a brief introduction into the assignments, followed by time to do the exercises on your computer. Both wired and wireless network access will be provided. There will be staff on hand to answer any questions. There will be plenty of opportunity to work on your favorite gene(s) with experts to help you over hurdles.

Session Plan:

1. Basic sequence analaysis
   Introduction to the PGA program. How to make sequence data useful? This session covers basic sequence analysis, sequence databases, and alignment tools.
2. Gene finding and genome annotation
   Learn about gene finding tools and their limitations. Look at annotated genome sequences. Given that you found your gene with lots of annotation, find out what you can do to expand and verify possibly conflicting annotation. Learn to use additional resources to build your confidence or distrust of the annotation.
3. Comparative genomics tools and SNP data analysis
   Learn to use the VISTA tools developed by the BerkeleyPGA to study conserved regions in cardiovascular genes. Introduction into SNP data analysis for comparative genomics.
4. Protein resources and tools
   Explore web-based tools for the characterization of protein sequence and structure using database, motif, and profile searching, as well as transmembrane prediction and multiple alignment tools. Phylogenomics: Use evolution to infer structural realtionships.
5. Using microarray data
   Introduction into microarray technology and data analysis for comparative genomics.
   Genetic and genomic tools to decipher atherogenic lipid metabolism.

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