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New algorithms for fixed-length approximate string matching and approximate circular string matching under the Hamming distance

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A Correction to this article was published on 20 March 2018

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Abstract

This paper proposes new algorithms for fixed-length approximate string matching and approximate circular string matching under the Hamming distance. Fixed-length approximate string matching and approximate circular string matching are special cases of approximate string matching and have numerous direct applications in bioinformatics and text searching. Firstly, a counter-vector-mismatches (CVM) algorithm is proposed to solve fixed-length approximate string matching with k-mismatches. The development of CVM algorithm is based on the parallel summation of counters located in the same machine word. Secondly, a parallel counter-vector-mismatches (PCVM) algorithm is proposed to accelerate CVM algorithm in parallel. The PCVM algorithm is integrated into two-level parallelisms that exploit not only word-level parallelism but also data parallelism via parallel environments such as multi-core processors and graphics processing units (GPUs). In the particular case of adopting GPUs, a shared-mem parallel counter-vector-mismatches (PCVMsmem) scheme can be implemented from PCVM algorithm. The PCVMsmem scheme can exploit the memory model of GPUs to optimize performance of PCVM algorithm. Finally, this paper shows several methods to adopt CVM and PCVM algorithms in case the input pattern is in circular structure. In the experiments with real DNA packages, our proposed algorithms and scheme work greatly faster than previous bit-vector-mismatches and parallel bit-vector-mismatches algorithms.

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  • 20 March 2018

    The funding information is missing in the Acknowledgements section of the original article. The correct wording is given below.

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Acknowledgements

We would like to thank Mr. Ji-Won Song, MS. candidate at School of EEE in Dankook University, who have helped us set up the Linux-based experimental environment using GPU.

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Authors and Affiliations

  1. School of Electronics and Electrical Engineering, Dankook University, Yongin-si, Gyeonggi-do, Republic of Korea

    ThienLuan Ho, Seung-Rohk Oh & HyunJin Kim

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  1. ThienLuan Ho
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  2. Seung-Rohk Oh
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  3. HyunJin Kim
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Correspondence to HyunJin Kim.

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Ho, T., Oh, SR. & Kim, H. New algorithms for fixed-length approximate string matching and approximate circular string matching under the Hamming distance. J Supercomput 74, 1815–1834 (2018). https://doi.org/10.1007/s11227-017-2192-6

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  • DOI: https://doi.org/10.1007/s11227-017-2192-6

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