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Review
. 2019 Apr-Jun;11(2):130-148.

Review of Different Sequence Motif Finding Algorithms

Fatma A Hashim  1 , Mai S Mabrouk  2 , Walid Al-Atabany  1
Affiliations
Review

Review of Different Sequence Motif Finding Algorithms

Fatma A Hashim et al. Avicenna J Med Biotechnol. 2019 Apr-Jun.

Abstract

The DNA motif discovery is a primary step in many systems for studying gene function. Motif discovery plays a vital role in identification of Transcription Factor Binding Sites (TFBSs) that help in learning the mechanisms for regulation of gene expression. Over the past decades, different algorithms were used to design fast and accurate motif discovery tools. These algorithms are generally classified into consensus or probabilistic approaches that many of them are time-consuming and easily trapped in a local optimum. Nature-inspired algorithms and many of combinatorial algorithms are recently proposed to overcome these problems. This paper presents a general classification of motif discovery algorithms with new sub-categories that facilitate building a successful motif discovery algorithm. It also presents a summary of comparison between them.

Keywords: Algorithms; Bioinformatics; Consensus; Gene expression regulation; Nucleotide motif; Protein binding.

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Figures

Figure 1.
Figure 1.
General block diagram of motif discovery technique.
Figure 2.
Figure 2.
Classification of motif discovery algorithms as enumerative, probabilistic, nature inspired and combinatorial types.
See this image and copyright information in PMC

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