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Unimodular Hypergraph for DNA Sequencing: A Polynomial Time Algorithm

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Abstract

The paper discusses a hypergraph-based polynomial time algorithm for constructing a DNA sequence corresponding to a given spectrum with no errors. The presence of n-ary relations in the expression of DNA sequencing led to the advent of hypergraphs in DNA sequencing. An efficient algorithm, unimodular hypergraph (UMHG), has been proposed for constructing unimodular hypergraph that represents the short-read DNA sequence of the given spectrum. The performance of the proposed algorithm is evaluated in comparison with prominent algorithms such as greedy, greedy (lag), ant colony optimization(ACO), multi-level ACO, enhanced genetic algorithm (GA), hybrid GA and tabu search against 40 instances. The proposed UMHG algorithm is found to outperform the other algorithms in terms of average similarity score. UMHG is significant in terms of minimum computing time, especially as the spectrum size increases computing time decreases considerably, owing to the unimodularity property.

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Acknowledgements

The authors thank SASTRA University for their financial and research support. Also, the authors thank the Department of Science and Technology—Fund for Improvement of S&T Infrastructure in Universities and Higher Educational Institutions Government of India (SR/FST/MSI-107/2015) for their financial support.

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Authors and Affiliations

  1. Discrete Mathematics Research Laboratory, Srinivasa Ramanujan Centre, SASTRA Deemed University, Kumbakonam, Tamil Nadu, India

    Swaminathan Venkatraman

  2. School of Computing, SASTRA Deemed University, Thanjavur, Tamil Nadu, India

    Gangothri Rajaram

  3. School of Humanities and Sciences, SASTRA Deemed University, Thanjavur, Tamil Nadu, India

    Kannan Krithivasan

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  1. Swaminathan Venkatraman
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  2. Gangothri Rajaram
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  3. Kannan Krithivasan
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Correspondence to Swaminathan Venkatraman.

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Venkatraman, S., Rajaram, G. & Krithivasan, K. Unimodular Hypergraph for DNA Sequencing: A Polynomial Time Algorithm. Proc. Natl. Acad. Sci., India, Sect. A Phys. Sci. 90, 49–56 (2020). https://doi.org/10.1007/s40010-018-0561-z

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  • DOI: https://doi.org/10.1007/s40010-018-0561-z

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