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GRaphical Footprint Based Alignment-Free Method (GRAFree) for Classifying the Species in Large-Scale Genomics

  • Aritra MahapatraEmail author
  • Jayanta Mukherjee
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11942)

Abstract

In our study, we propose to use novel features from mitochondrial genomic sequences reflecting their evolutionary traits by a novel GRaphical footprint based Alignment-Free method (GRAFree). These features are used to classify a set of species to different classes. A novel distance measure in the feature space is also proposed to measure the proximity of these species in the evolutionary processes. The distance function is found to be a metric. Further we model the evolutionary relationships of these classes by forming a phylogenetic tree. Experimentations were carried out with 157 species covering four different classes such as, Insecta, Actinopterygii, Aves, and Mammalia. We apply our proposed distance function on the selected feature vectors for three different graphical representations of genome. The inferred trees corroborate accepted evolutionary traits. This demonstrates that our proposed distance function and feature representation can be applied to classify different species and to capture the evolutionary relationships among their classes.

Keywords

Classification Phylogeny Mitochondrial genome Graphical footprint k-nearest neighbor classifier Hierarchical clustering 

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Department of Computer Science and EngineeringIndian Institute of TechnologyKharagpurIndia

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