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International Workshop on Algorithms and Computation

WALCOM 2018: WALCOM: Algorithms and Computation pp 183–194Cite as

A Simple, Fast, Filter-Based Algorithm for Circular Sequence Comparison

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 10755))

Abstract

This paper deals with the circular sequence comparison problem, a fundamental step in many important tasks in bioinformatics, which appears as an interesting problem in many biological contexts. Traditional algorithms for measuring approximation in sequence comparison are based on the notions of distance or similarity, and are generally computed through sequence alignment techniques. The circular sequence comparison (CSC) problem consists in finding all comparisons of the rotations of a pattern \(\mathcal {P}\) of length m in a text \(\mathcal {T}\) of length n. In CSC, we consider comparisons with minimum distance from circular pattern \(\mathcal {P}\) to text \(\mathcal {T}\) under the Hamming distance model. In this paper, we present a simple and fast filter-based algorithm to solve the CSC problem. We compare our algorithm with the state of the art algorithms and the results are found to be excellent. In particular, our algorithm runs almost twice as fast than the state of the art. Much of the efficiency of our algorithm can be attributed to its filters that are effective but extremely simple and lightweight.

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Notes

  1. 1.

    https://goo.gl/bKZ52e.

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Author information

Authors and Affiliations

  1. Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, 1215, Bangladesh

    Md. Aashikur Rahman Azim, Mohimenul Kabir & M. Sohel Rahman

Authors
  1. Md. Aashikur Rahman Azim
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  2. Mohimenul Kabir
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  3. M. Sohel Rahman
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Corresponding author

Correspondence to Md. Aashikur Rahman Azim .

Editor information

Editors and Affiliations

  1. Bangladesh University of Engineering and Technology, Dhaka, Bangladesh

    M. Sohel Rahman

  2. National University of Singapore , Singapore, Singapore

    Wing-Kin Sung

  3. Japan Advanced Institute of Science and Technology, Ishikawa, Japan

    Ryuhei Uehara

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Azim, M.A.R., Kabir, M., Rahman, M.S. (2018). A Simple, Fast, Filter-Based Algorithm for Circular Sequence Comparison. In: Rahman, M., Sung, WK., Uehara, R. (eds) WALCOM: Algorithms and Computation. WALCOM 2018. Lecture Notes in Computer Science(), vol 10755. Springer, Cham. https://doi.org/10.1007/978-3-319-75172-6_16

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  • DOI: https://doi.org/10.1007/978-3-319-75172-6_16

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-75171-9

  • Online ISBN: 978-3-319-75172-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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