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Browsing repeats in genomes: Pygram and an application to non-coding region analysis
Patrick Durand1, Frédéric Mahé, Anne-Sophie Valin
1IRISA/INRIA, Campus de Beaulieu, 35042 Rennes Cedex, France. Patrick.Durand@irisa.fr
BMC Bioinformatics
|October 28, 2006
Summary
Pygram is a new visualization tool for analyzing repeated sequences in genomes. This graphical browser helps researchers efficiently study genome organization and identify specific repeat patterns.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Repeated sequences significantly influence genome structure, function, dynamics, and evolution.
- Effective analysis of these sequences necessitates specialized methods, including advanced visualization techniques.
Purpose of the Study:
- Introduce Pygram, a novel visualization application designed for the investigation of repeated sequence organization within complete genome sequences.
- Enhance the efficiency of repeat analysis in genomic research.
Main Methods:
- Pygram projects data from a repeat index file onto analyzed sequences.
- Combines data projection with a query system to locate specific types of repeated sequences.
- Provides an efficient, graphical browsing interface for repeat exploration.
Main Results:
- Demonstrates Pygram's utility through an analysis of CRISPR structures in Archaea genomes.
- Successfully detected horizontal gene transfer events between Archaea and Viruses using the application.
- Highlights Pygram's capability in identifying and analyzing specific repeat properties.
Conclusions:
- Pygram offers a new visualization environment to streamline the analysis of repeated sequences.
- Aims to boost laboratory efficiency in studying repeat organization across single or multiple genomes.
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