Poster: Comparative Genomics
Abs #
913: Comparative and Functional Genomics Using PyMood
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Presenter: |
Matvienko, Marta , marta@allometra.com |
Authors | Matvienko, Marta (A) Kozik, Ivan (A) Meyers, Blake (B) Kozik, Alexander (A) | | Affiliations: |
(A): Allometra
(B): Delaware Biotechnology Institute
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| Web Site: | http://allometra.com | |
We have developed a desktop application for visualizing genomic data. The software is called PyMood, and it allows viewing the relationship between genes from multiple sources. It is adapted for displaying BLAST output results in 2D and 3D environments. The program accepts different kinds of data including expression data and mixed data sets. For visual data presentation PyMood uses the three primary colors: red, green, and blue. Every dataset gets one primary color assigned to it, and every data point in the dataset gets the color saturation degree according to its value. A typical use of the program would be to visualize the relationship between a query dataset and up to three other data sources, or to plot and sort the expression data. Using PyMood does not require advanced bioinformatics knowledge.
PyMood is cross-platform and works on Windows 2000/XP, Mac OS X 10.2, and Linux. The software description, screenshots, and example projects are available at http://allometra.com
To demonstrate the usage of PyMood for comparative genomics data analysis and visualization we compared Arabidopsis encoded proteins with yeast, human, and worm proteins. Arabidopsis specific proteins, proteins shared only between Arabidopsis and one or two other genomes, and the proteins shared between all four genomes have been identified. The project description and the lists of the extracted proteins are available for download at http://allometra.com/arabidopsis.shtml
To demonstrate the usage of PyMood for functional genomics we visualized the Arabidopsis MPSS expression data for five tissues: callus, flower, leaf, root, and silique. The data for pairwise library comparisons and for tissue specific transcripts are presented at http://allometra.com/mpss.shtml
