Big data analytics in bioinformatics: architectures, techniques, tools and issues

  • Hirak Kashyap
  • Hasin Afzal Ahmed
  • Nazrul Hoque
  • Swarup Roy
  • Dhruba Kumar Bhattacharyya
Review Article

Abstract

Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big data using the distributed and parallel computing technologies. Usually big data tools perform computation in batch mode and are not optimized for iterative processing and high data dependency among operations. In the recent years, parallel, incremental, and multi-view machine learning algorithms have been proposed. Similarly, graph-based architectures and in-memory big data tools have been developed to minimize I/O cost and optimize iterative processing. However, standard big data architectures are still lacking. Also appropriate tools are not available for many important bioinformatics problems, such as fast construction of co-expression and regulatory networks and salient module identification, detection of complexes over growing protein-protein interaction data, fast analysis of massive DNA, RNA, and protein sequence data, and fast querying on incremental and heterogeneous disease networks. This paper addresses the issues and challenges posed by several big data problems in bioinformatics, and gives an overview of the state of the art and the future research opportunities.

Keywords

Big data Bioinformatics Machine learning MapReduce Clustering Gene regulatory network 

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Copyright information

© Springer-Verlag Wien 2016

Authors and Affiliations

  • Hirak Kashyap
    • 1
  • Hasin Afzal Ahmed
    • 2
  • Nazrul Hoque
    • 2
  • Swarup Roy
    • 3
  • Dhruba Kumar Bhattacharyya
    • 2
  1. 1.Department of Computer Science, Donald Bren School of Information and Computer SciencesUniversity of California IrvineIrvineUSA
  2. 2.Department of Computer Science and EngineeringTezpur UniversityTezpurIndia
  3. 3.Department of Information TechnologyNorth Eastern Hill UniversityShillongIndia

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