title: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences.
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.
authors.affiliation: IEETA/DETI, University of Aveiro, Portugal.
authors.forename: Diogo
authors.initials: D
authors.lastname: Pratas
authors.affiliation: IEETA/DETI, University of Aveiro, Portugal.
authors.forename: Raquel M
authors.initials: RM
authors.lastname: Silva
authors.affiliation: IEETA/DETI, University of Aveiro, Portugal.
authors.forename: Armando J
authors.initials: AJ
authors.lastname: Pinho
authors.affiliation: IEETA/DETI, University of Aveiro, Portugal.
authors.forename: Paulo J S G
authors.initials: PJ
authors.lastname: Ferreira
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D015321:Gene Rearrangement; D023281:Genomics / Q000379:methods*; D006801:Humans; D064878:Web Browser