Title: SyDiG: uncovering Synteny in Distant Genomes

Authors: Geraldine Jean, Macha Nikolski

Addresses: Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen, Germany. ' CNRS/LaBRI, Universite Bordeaux 1, 351 cours de la Liberation, 33405 Talence Cedex, France

Abstract: Current methods for detecting synteny work well for genomes with high degrees of inter- and intra-species chromosomal homology, such as mammals. This paper presents a new algorithm for synteny computation that is well suited to genomes covering a large evolutionary span. It is based on a three-step process: identification of initial microsyntenic homologous regions, extension of homologous boundaries and reconstruction of syntenic blocks by identification of groups of homologous genomic segments that are conserved in every subject genome. Our method performs as well as GRIMM-Synteny on mammalian genomes, and outperforms it for clades with much greater evolutionary distances such as the Hemiascomycetous yeasts.

Keywords: synteny computation; algorithms; multiplicon; bioinformatics; clades; evolution; microsyntenic homologous regions; homologous boundaries; syntenic blocks; homologous genomic segments; genomes.

DOI: 10.1504/IJBRA.2011.039169

International Journal of Bioinformatics Research and Applications, 2011 Vol.7 No.1, pp.43 - 62

Published online: 24 Jan 2015 *

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