Gene Cluster Analysis with GenomeVectorizer

Naidele Katrumane Manjunath and Elena KochetkovaPresented by Rohan Vibhandik
San Jose State University, San Jose, CA, USA
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Genome study requires information pertaining to every gene in a chromosome. Visualising information of how a gene is related to other genes in the same chromosome or to genes in other chromosomes will make the understanding of the relations more clear. Available genome visualization tools provide mainly the view of the overall genome [Websites 2,3,4] and some tools have features like zooming into a particular chromosome and viewing the gene in detail [2].

In this paper we present a new capability of "Genome Vectorizer" (formerly known as "Genome Pixelizer SVG-fied") where a gene can be dragged out of a chromosome for more detailed analysis. This feature is an extension to ‘Genome Pixelizer SVG-fied’ which is a genome visualization tool that has been developed by Elena Kochetkova [1].

"Genome Vectorizer" is a re-designed version of GenomePixelizer, written in 2002 in TCL/TK, a tool that allows for the detection of duplication events in genomes. It capitalizes on the benefits of using XML, XSLT, and SVG technologies combined with JavaScript scripting “to provide users with simpler interface, maximized interactivity; as well as, improved efficiency of genetic data analysis” [1].

Gene dragging capability, which is presented in this paper, will provide users much more interactivity, since often the users focus on a particular gene rather than the entire chromosome. Once the common genes are matched between chromosomes the user can drag the gene of interest out along with all the details pertaining to it.

Bibliography

Articles

[1] Elena Kochetkova. “GenomePixelizer SVG-fied”.

[2] Kozik, A., Kochetkova, E., Michelmore, R. GenomePixelizer – a visualization program for comparative genomics within and between species. Bioinformatics 2002. 18:335-336.

[3] Benjamin G.S. Horsman. “A New Horizon for SVG: Bioinformatics” . 2003.

[4] Dr. William Rutherford. “SVG Bioinformatics Collaboration Tool”. 2003.

[5] Christopher T Lewis, Steve Karcz, Andrew Sharpe, and A.P. Parkin Isobel. “BioViz: Genome Viewer”. Development of an SVG GUI for the visualization of genome data. 07-Nov-2003.

[6] Andrei L. Turinsky, Andrew C. Ah-Seng, Paul M. K Gordon, Julie N. Stromer, Morgan L. Taschuk, Emily W. Xu, Christoph W. Sensen,. “ Bioinformatics visualization and integration with open standards: The Bluejay genomic browser ”. Copyright © 2004 Bioinformation Systems e.V.

Websites

[1] GD::SVG – Seamlessly enable SVG output from GD scripts. Todd W. Harris. Copyright © 2003 Todd Harris and the Cold Spring Harbor Laboratory. "http://toddot.net/projects/GD-SVG/index.shtml"

[2] Argo Genome Browser. BROAD Institute. 7 July 2008. 22 May 2009. "http://www.broad.mit.edu/annotation/argo/"

[3] Circos. May 22 2009. "http://mkweb.bcgsc.ca/circos/"

[4] Alfresco. Sanger Institute. 27 May 2008. 22 May 2009. "http://www.sanger.ac.uk/Software/Alfresco/"

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