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Title: Genomic distance under gene substitutions
Authors: Machado, Raphael Carlos Santos
Braga, Marília Dias Vieira
Ribeiro, Leonardo Costa
Stoye, Jens
Keywords: Genomas
Biologia molecular
Issue Date: 2011
Citation: BRAGA, Marília D. V. et al. Genomic distance under gene substitutions. BMC Bioinformatics, v. 12, 2011.
Abstract: Background: The distance between two genomes is often computed by comparing only the common markers between them. Some approaches are also able to deal with non-common markers, allowing the insertion or the deletion of such markers. In these models, a deletion and a subsequent insertion that occur at the same position of the genome count for two sorting steps. Results: Here we propose a new model that sorts non-common markers with substitutions, which are more powerful operations that comprehend insertions and deletions. A deletion and an insertion that occur at the same position of the genome can be modeled as a substitution, counting for a single sorting step. Conclusions: Comparing genomes with unequal content, but without duplicated markers, we give a linear time algorithm to compute the genomic distance considering substitutions and double-cut-and-join (DCJ) operations. This model provides a parsimonious genomic distance to handle genomes free of duplicated markers, that is in practice a lower bound to the real genomic distances. The method could also be used to refine orthology assignments, since in some cases a substitution could actually correspond to an unannotated orthology.
Description: 9 p. : il.
Document type: Artigo / Article
Unit: Divisão de Metrologia em Telecomunicações - Ditel
Appears in Collections:DITEL | Artigos publicados em periódicos internacionais

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