Genomic distance under gene substitutions

• Autor(a) principal: Machado, Raphael Carlos Santos
• Data de Publicação: 2011
• Outros Autores: Braga, Marília Dias Vieira, Ribeiro, Leonardo Costa, Stoye, Jens
• Tipo de documento: Artigo
• Idioma: eng
• Título da fonte: Repositório Institucional do INMETRO
• Texto Completo: http://hdl.handle.net/10926/1328

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.