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Nature-inspired novel Cuckoo Search Algorithm for genome sequence assembly

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Abstract

This study aims to produce a novel optimization algorithm, called the Cuckoo Search Algorithm (CS), for solving the genome sequence assembly problem. Assembly of genome sequence is a technique that attempts to rebuild the target sequence from the collection of fragments. This study is the first application of the CS for DNA sequence assembly problem in the literature. The algorithm is based on the levy flight behaviour and brood parasitic behaviour. The CS algorithm is employed to maximize the overlap score by reconstructing the original DNA sequence. Experimental results show the ability of the CS to find better optimal genome assembly. To check the efficiency of the proposed technique the results of the CS is compared with one of the well known evolutionary algorithms namely, particle swarm optimization (PSO) and its variants.

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Acknowledgements

We thank the Coimbatore Institute of Technology, Coimbatore for providing us necessary facilities and support.We are thankful to Dr. Raja CMugasimangalam, Genome Informatics team and Microarray Design Team at Genotypic Technology Private Limited, Bangalore, for the helpful discussions on genome fragment assembly.

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Authors and Affiliations

  1. Department of Electronics and Communication Engineering, Coimbatore Institute of Technology, Coimbatore, 641 014, India

    R INDUMATHY & S UMA MAHESWARI

  2. Department of Information Technology, PSG College of Technology, Coimbatore, 641 004, India

    G SUBASHINI

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  1. R INDUMATHY
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  2. S UMA MAHESWARI
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  3. G SUBASHINI
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Correspondence to R INDUMATHY.

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INDUMATHY, R., UMA MAHESWARI, S. & SUBASHINI, G. Nature-inspired novel Cuckoo Search Algorithm for genome sequence assembly. Sadhana 40, 1–14 (2015). https://doi.org/10.1007/s12046-014-0300-3

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