Genomic distance under gene substitutions

BMC Bioinformatics

Proceedings

Jens Stoye¹  Marília D V Braga²  Leonardo C Ribeiro²  Raphael Machado² 

[1] AG Genominformatik, Technische Fakultät, Universität Bielefeld, 33594, Bielefeld, Germany;Instituto Nacional de Metrologia, Qualidade e Tecnologia, Duque de Caxias, 25250-020, Brazil;

关键词: Linear Time Algorithm;    Adjacency Graph;    Triangular Inequality;    Genomic Distance;    Unique Marker;   

DOI  :  10.1186/1471-2105-12-S9-S8

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsHere 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.ConclusionsComparing 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.

【 授权许可】

CC BY   
© Braga et al; licensee BioMed Central Ltd. 2011