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Regulatory Motif Identification in Biological Sequences: An Overview of Computational Methodologies

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Advances in Enzyme Biotechnology

Abstract

The transcription factor binding sites (TFBS), also called as motifs, are short, recurring patterns in DNA sequences that are presumed to have a biological function. Identification of the motifs from the promoter region of the genes is an important and challenging problem, specifically in the eukaryotic genomes. In this chapter, an overview of motif identification methods has been presented. The computational methods for motif identification are classified as enumerative methods, probabilistic methods, phylogeny-based methods, and machine learning methods. The chapter also presents the standard evaluation scheme for accuracy of prediction.

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Authors and Affiliations

  1. Department of Computer Science and Engineering, Birla Institute of Technology, Mesra Extension Center Jaipur, 27, Malviya Industrial Area, Jaipur, 302017, Rajasthan, India

    Shripal Vijayvargiya

  2. Department of Biotechnology, Birla Institute of Technology (Deemed University), Extension Centre, Jaipur, India

    Shripal Vijayvargiya

  3. Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, M.D. University, Rohtak, India

    Pratyoosh Shukla

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  1. Shripal Vijayvargiya
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Correspondence to Shripal Vijayvargiya .

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  1. Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India

    Pratyoosh Shukla

  2. Department of Biochemistry,, Rhodes University, Grahamstown, South Africa

    Brett I. Pletschke

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Vijayvargiya, S., Shukla, P. (2013). Regulatory Motif Identification in Biological Sequences: An Overview of Computational Methodologies. In: Shukla, P., Pletschke, B. (eds) Advances in Enzyme Biotechnology. Springer, New Delhi. https://doi.org/10.1007/978-81-322-1094-8_8

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