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Choice of Metric Divergence in Genome Sequence Comparison

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Abstract

The paper introduces a novel probability descriptor for genome sequence comparison, employing a generalized form of Jensen-Shannon divergence. This divergence metric stems from a one-parameter family, comprising fractions up to a maximum value of half. Utilizing this metric as a distance measure, a distance matrix is computed for the new probability descriptor, shaping Phylogenetic trees via the neighbor-joining method. Initial exploration involves setting the parameter at half for various species. Assessing the impact of parameter variation, trees drawn at different parameter values (half, one-fourth, one-eighth). However, measurement scales decrease with parameter value increments, with higher similarity accuracy corresponding to lower scale values. Ultimately, the highest accuracy aligns with the maximum parameter value of half. Comparative analyses against previous methods, evaluating via Symmetric Distance (SD) values and rationalized perception, consistently favor the present approach's results. Notably, outcomes at the maximum parameter value exhibit the most accuracy, validating the method's efficacy against earlier approaches.

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No datasets were generated or analysed during the current study.

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Authors and Affiliations

  1. Information Technology, Narula Institute of Technology, Kolkata, West Bengal, India

    Soumen Ghosh

  2. Computer Science & Engineering, Narula Institute of Technology, Kolkata, West Bengal, India

    Jayanta Pal

  3. Electronics & Communication Engineering, National Institute of Technology, Durgapur, West Bengal, India

    Bansibadan Maji

  4. DEIM, University of Tuscia, Largo Dell’Universita, 01100, Viterbo, Italy

    Carlo Cattani

  5. Pure Mathematics, University of Calcutta, Kolkata, West Bengal, India

    Dilip Kumar Bhattacharya

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  1. Soumen Ghosh
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  2. Jayanta Pal
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  4. Carlo Cattani
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  5. Dilip Kumar Bhattacharya
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Contributions

SG: Design and development of the work and finalization of draft. JP: Data collection, analysis and interpretation. BM: Initial drafting the article. CC: Critical revision of the article after final draft. DKB: Concepttion of the work and critical revision of the article after final draft.

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Correspondence to Soumen Ghosh.

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Ghosh, S., Pal, J., Maji, B. et al. Choice of Metric Divergence in Genome Sequence Comparison. Protein J 43, 259–273 (2024). https://doi.org/10.1007/s10930-024-10189-x

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