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Int J Bioinform Res Appl. 2011;7(1):43-62.

SyDiG: uncovering Synteny in Distant Genomes.

Author information

1
Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen, Germany. geraldine.jean@tuebingen.mpg.de

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.

PMID:
21441096
DOI:
10.1504/IJBRA.2011.039169
[Indexed for MEDLINE]

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