c-GAMMA: Comparative Genome Analysis of Molecular Markers

Pierre Peterlongo 1, * Jacques Nicolas 1 Dominique Lavenier 1 Raoul Vorc'H 1 Joël Querellou 2
* Corresponding author
1 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
Abstract : Discovery of molecular markers for efficient identification of living organisms remains a challenge of high interest. The diversity of species can now be observed in details with low cost genomic sequences produced by new generation of sequencers. A method, called c-GAMMA, is proposed. It formalizes the design of new markers for such data. It is based on a series of filters on forbidden pairs of words, followed by an optimization step on the discriminative power of candidate markers. First results are presented on a set of microbial genomes. The importance of further devel- opments are stressed to face the huge amounts of data that will soon become available in all kingdoms of life.
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Pierre Peterlongo, Jacques Nicolas, Dominique Lavenier, Raoul Vorc'H, Joël Querellou. c-GAMMA: Comparative Genome Analysis of Molecular Markers. Pattern Recognition in Bioinformatics, Sep 2009, Sheffield, United Kingdom. pp.255-269, ⟨10.1007/978-3-642-04031-3_23⟩. ⟨inria-00425373⟩

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