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Erratum published on 30 August 2020, see Symmetry 2020, 12(9), 1433.
Open AccessArticle

A Modified Median String Algorithm for Gene Regulatory Motif Classification

Department of Computer Science and Engineering, Chittagong University of Engineering and Technology, Chittagong 4349, Bangladesh
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Symmetry 2020, 12(8), 1363; https://doi.org/10.3390/sym12081363
Received: 25 July 2020 / Revised: 10 August 2020 / Accepted: 12 August 2020 / Published: 14 August 2020
Consensus string is a significant feature of a deoxyribonucleic acid (DNA) sequence. The median string is one of the most popular exact algorithms to find DNA consensus. A DNA sequence is represented using the alphabet Σ= {a, c, g, t}. The algorithm generates a set of all the 4l possible motifs or l-mers from the alphabet to search a motif of length l. Out of all possible l-mers, it finds the consensus. This algorithm guarantees to return the consensus but this is NP-complete and runtime increases with the increase in l-mer size. Using transitional probability from the Markov chain, the proposed algorithm symmetrically generates four subsets of l-mers. Each of the subsets contains a few l-mers starting with a particular letter. We used these reduced sets of l-mers instead of using 4ll-mers. The experimental result shows that the proposed algorithm produces a much lower number of l-mers and takes less time to execute. In the case of l-mer of length 7, the proposed system is 48 times faster than the median string algorithm. For l-mer of size 7, the proposed algorithm produces only 2.5% l-mer in comparison with the median string algorithm. While compared with the recently proposed voting algorithm, our proposed algorithm is found to be 4.4 times faster for a longer l-mer size like 9. View Full-Text
Keywords: DNA consensus; markov chain; median string algorithm; pattern recognition DNA consensus; markov chain; median string algorithm; pattern recognition
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MDPI and ACS Style

Kaysar, M.S.; Khan, M.I. A Modified Median String Algorithm for Gene Regulatory Motif Classification. Symmetry 2020, 12, 1363. https://doi.org/10.3390/sym12081363

AMA Style

Kaysar MS, Khan MI. A Modified Median String Algorithm for Gene Regulatory Motif Classification. Symmetry. 2020; 12(8):1363. https://doi.org/10.3390/sym12081363

Chicago/Turabian Style

Kaysar, Mohammad S.; Khan, Mohammad I. 2020. "A Modified Median String Algorithm for Gene Regulatory Motif Classification" Symmetry 12, no. 8: 1363. https://doi.org/10.3390/sym12081363

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