An alignment-free method to find and visualise rearrangements between pairs of DNA sequences

Pratas D, Silva RM, Pinho AJ, Ferreira PJSG


Scientific Reports 5(10203), May 2015
DOI: 10.1038/srep10203

Abstract

Species evolution is indirectly registered in their genomic structure. The emergence and advances in sequencing technology provided a way to access genome information, namely to identify and study evolutionary macro-events, as well as chromosome alterations for clinical purposes. This paper describes a completely alignment-free computational method, based on a blind unsupervised approach, to detect large-scale and small-scale genomic rearrangements between pairs of DNA sequences. To illustrate the power and usefulness of the method we give complete chromosomal information maps for the pairs human-chimpanzee and human-orangutan. The tool by means of which these results were obtained has been made publicly available and is described in detail.

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