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A Novel Method of Characterizing DNA Sequences Based on Complete Composition and Position Vector

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Complete composition vector (CPV) is an effective and alignment-free method to characterize DNA sequences according to the distribution of short words. By introduced position information of the short words, a called complete composition and position vector (CCPV) method has been proposed in this paper, which is described to infer evolutionary relationships between species using their complete genomic sequences. After presenting the method, it is applied to classify chromosomes according to the distances among different sequences firstly. And then it is used to build the phylogenetic tree of 48 HEV (Hepatitis E virus) genome sequences. Finally, the CCPV method is also to analyze the phylogenetic relationships of 24 complete genome sequences of coronaviruses. Our results indicate that the proposed method can serve as an alternative to rapidly construct phylogenetic trees and infer evolutionary relationships.
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Keywords: ALIGNMENT-FREE; COMPLETE COMPOSITION; PHYLOGENETIC TREE; POSITION VECTOR; SEQUENCE COMPARISON

Document Type: Research Article

Publication date: August 1, 2013

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  • Bionanoscience attempts to harness various functions of biological macromolecules and integrate them with engineering for technological applications. It is based on a bottom-up approach and encompasses structural biology, biomacromolecular engineering, material science, and engineering, extending the horizon of material science. The journal aims at publication of (i) Letters (ii) Reviews (3) Concepts (4) Rapid communications (5) Research papers (6) Book reviews (7) Conference announcements in the interface between chemistry, physics, biology, material science, and technology. The use of biological macromolecules as sensors, biomaterials, information storage devices, biomolecular arrays, molecular machines is significantly increasing. The traditional disciplines of chemistry, physics, and biology are overlapping and coalescing with nanoscale science and technology. Currently research in this area is scattered in different journals and this journal seeks to bring them under a single umbrella to ensure highest quality peer-reviewed research for rapid dissemination in areas that are in the forefront of science and technology which is witnessing phenomenal and accelerated growth.
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