Pyramid diagram: visualizing the organization of repetitive sequences in genomes.

Patrick Durand 1 Frédéric Mahé 2 Anne-Sophie Valin 1 Jacques Nicolas 1
1 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
Abstract : We introduce a new visualization method, the pyramid diagram, or pygram, capable of summarizing the hierarchical organization of repetitive structures in genome sequences. Pygrams improve over previous methods because they clearly display complex patterns of repeats located either within a single sequence or between several sequences, and are founded on the well defined notion of maximal repeat. This report describes the design and implementation of Pyramid, a tool producing pygrams, and details some applications of the visualization method in Virus and Archaea genomics.
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https://hal.archives-ouvertes.fr/hal-00129758
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Submitted on : Thursday, February 8, 2007 - 4:24:55 PM
Last modification on : Monday, April 29, 2019 - 2:30:44 PM

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  • HAL Id : hal-00129758, version 1

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Patrick Durand, Frédéric Mahé, Anne-Sophie Valin, Jacques Nicolas. Pyramid diagram: visualizing the organization of repetitive sequences in genomes.. 2005. ⟨hal-00129758⟩

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