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|Title: ||Genomic distance under gene substitutions|
|Authors: ||Machado, Raphael Carlos Santos|
Braga, Marília Dias Vieira
Ribeiro, Leonardo Costa
|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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