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.
Highlights
Species evolution is indirectly registered in their genomic structure
Structural genomic rearrangements are a major source of intra- and inter-species variation
Many leukaemia patients present a reciprocal translocation between chromosomes 9 and 22, known as the Philadelphia chromosome
Summary
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. Many leukaemia patients present a reciprocal translocation between chromosomes 9 and 22, known as the Philadelphia chromosome This produces BCR-ABL fusion proteins that are constitutively active tyrosine kinases, contributing to tumour growth and proliferation[2]. Another striking example is the human inversion polymorphism in the 17q21 region, which contains the neurodegenerative disorder-associated gene MAPT (microtubule associated protein Tau). In some groups, such as the great apes, access to samples is often difficult, e.g. due to ethical reasons These approaches can be time-consuming, expensive, or lack resolution, as opposed to computational solutions[8]. Derived scientific insights from genomic sequences, including the conserved distribution of genes on the chromosomes of different species or synteny, have been mostly explored using sequence www.nature.com/scientificreports/
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