DNA barcoding using particle swarm optimization on apache spark SQL case study: DNA of covid-19

Document Type : Research Paper

Authors

1 Department of Computer Science Education, Universitas Pendidikan Indonesia, Indonesia

2 Faculty of Computer and Mathematical Sciences, University Teknologi MARA Cawangan Melaka Kampus Jasin, Melaka, Malaysia

Abstract

The objective of this research is to design and implement a computational model to determine DNA barcodes by utilizing the Particle Swarm Optimization (PSO) algorithms implemented on Big Data Platforms, namely Apache Hadoop and Apache Spark. The steps are as follows: (i) inputting DNA sequences to Hadoop Distributed File System (HDFS) in Apache Hadoop, (ii) pre-processing data, (iii) implementing PSO by utilizing the User Defined Function (UDF) in Apache Spark, (iv) collecting results and saving to HDFS. After obtaining the computational model, two following simulations have been done: the first scenario is using 4 cores and several worker nodes, meanwhile, the second one consists of a cluster with 2 worker nodes and several cores. In terms of computational time, the results show a significant acceleration between standalone and big data platforms with both experimental scenarios. This study proves that the computational model built on the big data platform shows the development of features and acceleration of previous research.

Keywords

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Volume 12, Special Issue
December 2021
Pages 1561-1572
  • Receive Date: 16 August 2021
  • Revise Date: 21 September 2021
  • Accept Date: 03 November 2021