Browsing repeats in genomes: Pygram and an application to non-coding region analysis.
BACKGROUND
A large number of studies on genome sequences have revealed the major role played by repeated sequences in the structure, function, dynamics and evolution of genomes. In-depth repeat analysis requires specialized methods, including visualization techniques, to achieve optimum exploratory power.


RESULTS
This article presents Pygram, a new visualization application for investigating the organization of repeated sequences in complete genome sequences. The application projects data from a repeat index file on the analysed sequences, and by combining this principle with a query system, is capable of locating repeated sequences with specific properties. In short, Pygram provides an efficient, graphical browser for studying repeats. Implementation of the complete configuration is illustrated in an analysis of CRISPR structures in Archaea genomes and the detection of horizontal transfer between Archaea and Viruses.


CONCLUSIONS
By proposing a new visualization environment to analyse repeated sequences, this application aims to increase the efficiency of laboratories involved in investigating repeat organization in single genomes or across several genomes.
Durand
Patrick
P
IRISA/INRIA, Campus de Beaulieu, 35042 Rennes Cedex, France. Patrick.Durand@irisa.fr
Mahé
Frédéric
F
Valin
Anne-Sophie
AS
Nicolas
Jacques
J
D003062:Codon / Q000737:chemistry / Q000235:genetics; D020745:Genome, Archaeal / Q000235:genetics*; D016679:Genome, Viral / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D012984:Software
D003062:Codon