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A Lightweight Algorithm for Computing BWT from Suffix Array in Disk

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Parallel Architecture, Algorithm and Programming (PAAP 2017)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 729))

Abstract

The Burrows-Wheeler transform (BWT) and the suffix array (SA) of an input string are important data structures widely used in modern bioinformatics researches such as full-text search, alignment etc. In this paper, we present a lightweight external memory algorithm for computing the BWT from a given suffix array and the input string. The algorithm has a linear I/O complexity O(n) and a workspace of at most n/2 integers. An experiment study is conducted to evaluate the time and space performance of the proposed algorithm on a number of realistic datasets. The experimental results are consistent with the theoretical complexities of the algorithm.

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Acknowledgments

The work of G. Nong was supported by the Guangzhou Science and Technology Program grant 201707010165 and the Project of DEGP grant 2014KTSCX007.

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Authors and Affiliations

  1. Department of Computer Science, Sun Yat-sen University, Guangzhou, China

    Jing Yi Xie, Bin Lao & Ge Nong

  2. SYSU-CMU Shunde International Joint Research Institute, Shunde, China

    Ge Nong

Authors
  1. Jing Yi Xie
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  2. Bin Lao
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  3. Ge Nong
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Corresponding author

Correspondence to Ge Nong .

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Editors and Affiliations

  1. Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu, China

    Guoliang Chen

  2. Sun Yat-sen University, Guangzhou, Guangdong, China

    Hong Shen

  3. Hainan University, Haikou, Hainan, China

    Mingrui Chen

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© 2017 Springer Nature Singapore Pte Ltd

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Xie, J.Y., Lao, B., Nong, G. (2017). A Lightweight Algorithm for Computing BWT from Suffix Array in Disk. In: Chen, G., Shen, H., Chen, M. (eds) Parallel Architecture, Algorithm and Programming. PAAP 2017. Communications in Computer and Information Science, vol 729. Springer, Singapore. https://doi.org/10.1007/978-981-10-6442-5_25

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  • DOI: https://doi.org/10.1007/978-981-10-6442-5_25

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  • Publisher Name: Springer, Singapore

  • Print ISBN: 978-981-10-6441-8

  • Online ISBN: 978-981-10-6442-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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