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Fast Algorithm for the Minimum Chebyshev Distance in RNA Secondary Structure

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Broadband Communications, Networks, and Systems (Broadnets 2019)

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Abstract

Minimum Chebyshev distance computation between base-pair and structures cost most time while comparing RNA secondary structures. We present a fast algorithm for speeding up the minimum Chebyshev distance computation. Based on the properties of RNA dot plots and Chebyshev distance, this algorithm uses binary search to reduce the size of base pairs and compute Chebyshev distances rapidly. Compared with O(n) time complexity of the original algorithm, the new one takes nearly [O(log2n), O(1)] time.

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Authors and Affiliations

  1. Yanshan University, Hebei, 066004, China

    Tiejun Ke, Changwu Wang, Wenyuan Liu & Jiaomin Liu

Authors
  1. Tiejun Ke
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  2. Changwu Wang
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  3. Wenyuan Liu
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  4. Jiaomin Liu
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Corresponding author

Correspondence to Changwu Wang .

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Editors and Affiliations

  1. Xidian University, Xi'an, China

    Qingshan Li

  2. Xidian University, Xi'an, China

    Shengli Song

  3. Xidian University, Xi'an, China

    Rui Li

  4. Xidian University, Xi'an, China

    Yueshen Xu

  5. Xi’an Jiaotong University, Xi'an, Shaanxi, China

    Wei Xi

  6. Shanghai University, Shanghai, China

    Honghao Gao

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© 2019 ICST Institute for Computer Sciences, Social Informatics and Telecommunications Engineering

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Ke, T., Wang, C., Liu, W., Liu, J. (2019). Fast Algorithm for the Minimum Chebyshev Distance in RNA Secondary Structure. In: Li, Q., Song, S., Li, R., Xu, Y., Xi, W., Gao, H. (eds) Broadband Communications, Networks, and Systems. Broadnets 2019. Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering, vol 303. Springer, Cham. https://doi.org/10.1007/978-3-030-36442-7_16

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  • DOI: https://doi.org/10.1007/978-3-030-36442-7_16

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-36441-0

  • Online ISBN: 978-3-030-36442-7

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