DUC-Curve, a highly compact 2D graphical representation of DNA sequences and its application in sequence alignment

Yushuang Li, Qian Liu and Xiaoqi Zheng

Physica A: Statistical Mechanics and its Applications, 2016, vol. 456, issue C, 256-270

Abstract: A highly compact and simple 2D graphical representation of DNA sequences, named DUC-Curve, is constructed through mapping four nucleotides to a unit circle with a cyclic order. DUC-Curve could directly detect nucleotide, di-nucleotide compositions and microsatellite structure from DNA sequences. Moreover, it also could be used for DNA sequence alignment. Taking geometric center vectors of DUC-Curves as sequence descriptor, we perform similarity analysis on the first exons of β-globin genes of 11 species, oncogene TP53 of 27 species and twenty-four Influenza A viruses, respectively. The obtained reasonable results illustrate that the proposed method is very effective in sequence comparison problems, and will at least play a complementary role in classification and clustering problems.

Keywords: Graphical representation; DNA sequence; DUC-Curve; Sequence alignment; Sequence comparison (search for similar items in EconPapers)
Date: 2016
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Citations: View citations in EconPapers (1)

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Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:456:y:2016:i:c:p:256-270

DOI: 10.1016/j.physa.2016.03.061

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