AROHap: An effective algorithm for single individual haplotype reconstruction based on asexual reproduction optimization |
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| Institution: | 1. Department of Metabolic & Structural Biology, CSIR-Central Institute of Medicinal & Aromatic Plants, P.O.-CIMAP, Kukrail Picnic Spot Road, Lucknow, 226015, Uttar Pradesh, India;2. Academy of Scientific & Innovative Research (AcSIR), CSIR-CIMAP Campus, CSIR-Central Institute of Medicinal & Aromatic Plants, P.O.-CIMAP, Lucknow, 226015, Uttar Pradesh, India;1. Department of Biotechnology, PRIST University, Thanjavur, 613403, Tamil Nadu, India;2. Centre for Research and Development, PRIST University, Thanjavur, 613403, Tamil Nadu, India;3. Centre for Functionalized Magnetic Material (FunMagMa), Immanuel Kant Baltic Federal University, Kaliningrad, 236041, Russia;4. Dept of Biochemistry and Heamatology, Thyrocare Technologies Ltd, Navi Mumbai, Maharastra, India;1. Key Laboratory of Synthetic Rubber, Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences, Changchun 130022, PR China;2. School of Life Science, Jilin University, Changchun 130012, PR China;3. University of Chinese Academy of Sciences, Beijing 100049, PR China |
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| Abstract: | In this paper, a method for single individual haplotype (SIH) reconstruction using Asexual reproduction optimization (ARO) is proposed. Haplotypes, as a set of genetic variations in each chromosome, contain vital information such as the relationship between human genome and diseases. Finding haplotypes in diploid organisms is a challenging task. Experimental methods are expensive and require special equipment. In SIH problem, we encounter with several fragments and each fragment covers some parts of desired haplotype. The main goal is bi-partitioning of the fragments with minimum error correction (MEC). This problem is addressed as NP-hard and several attempts have been made in order to solve it using heuristic methods. The current method, AROHap, has two main phases. In the first phase, most of the fragments are clustered based on a practical metric distance. In the second phase, ARO algorithm as a fast convergence bio-inspired method is used to improve the initial bi-partitioning of the fragments in the previous step. AROHap is implemented with several benchmark datasets. The experimental results demonstrate that satisfactory results were obtained, proving that AROHap can be used for SIH reconstruction problem. |
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| Keywords: | Bioinformatics Haplotype reconstruction Minimum error correction Asexual reproduction optimization |
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