Paul Van Eck
Paul Van Eck
Year: 2012

Pedigree Visualization and Genome Referencing

The Sol Genomics Network (SGN) database contains genealogical information on genetic stocks, but the SGN website lacked a friendly way of showcasing this information. To remedy this, a pedigree visualization tool was created and integrated into the site using Perl, HTML, JavaScript, and GraphViz. Pedigree charts show the genetic history of an organism over several generations, so such a tool will allow plant breeders and biologists to easily view the genealogy of a subject of interest. This allows for better integration of information from historical breeding records and genomic resources.

In a separate project, in an effort to have more plant genome resources available on SGN, the rice and grape genomes were loaded into the SGN database and configured to work with GBrowse, a tool for displaying and interacting with genomic annotations. Having these available is a great resource for plant genome analysis. Similarly, gene families, which are sets genes with similar sequences, were also loaded into GBrowse for easy viewing. These families consisted of potato, grape, tomato, arabidopsis, and rice. Paralog and ortholog groups derived from the gene families were also used in an attempt to detect genome duplications and their pattern of distribution in the genome.

My Experience

This summer internship at BTI was undoubtedly a worthwhile and lasting experience. I was given an excellent opportunity to relate my computer science major to the field of biology, and with the assistance of a wonderful group of mentors, I was able to learn a lot about what bioinformaticians do. Even if I do not continue studying bioinformatics, much of the knowledge I gained is still highly relevant to my major. I am much more proficient in working on Unix systems, and can now more comfortably work with Perl and JavaScript. Through this internship, I met many fantastic people, got to explore much of Ithaca, and had an overall unforgettable time.

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