Skip to main content
SpringerLink
Log in

Searching and Indexing Circular Patterns

  • Chapter
  • First Online:
Algorithms for Next-Generation Sequencing Data

Abstract

Circular DNA sequences can be found in viruses, as plasmids in archaea and bacteria, and in the mitochondria and plastids of eukaryotic cells. Hence, circular sequence comparison finds applications in several biological contexts (Barton et al., Experimental algorithms. Lecture notes in computer science, vol 9125, pp 247–258, 2015; Barton et al., Algorithms Mol Biol 9(9):2014; Uliel et al., Protein Eng 14(8):533–542, 2001). This motivates the design of efficient algorithms (Barton et al., Language and automata theory and applications. Lecture notes in computer science, vol 8977, pp 85–96. Springer, Berlin, 2015) and data structures (Hon et al., Combinatorial pattern matching. Lecture notes in computer science, vol 7922, pp 142–152. Springer, Berlin/Heidelberg, 2013) that are devoted to the specific comparison of circular sequences, as they can be relevant in the analysis of organisms with such structure (Grossi et al., Proceedings of algorithms in bioinformatics - 15th international workshop, WABI 2015, Atlanta, GA, Sept 10–12, 2015. Lecture notes in computer science, vol 9289, pp 203–216. Springer, Berlin, 2015; Gusfield, Algorithms on strings, trees, and sequences - computer science and computational biology. Cambridge University Press, Cambridge, 1997).

This chapter was written when Rahman was on a sabbatical leave from BUET.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 159.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Aho, A.V., Corasick, M.J.: Efficient string matching: an aid to bibliographic search. Commun. ACM 18(6), 333–340 (1975)

    Article  MathSciNet  MATH  Google Scholar 

  2. Athar, T., Barton, C., Bland, W., Gao, J., Iliopoulos, C.S., Liu, C., Pissis, S.P.: Fast circular dictionary-matching algorithm. Math. Struct. Comput. Sci. FirstView, 1–14 (2015)

    Google Scholar 

  3. Barton, C., Iliopoulos, C.S., Pissis, S.P.: Circular string matching revisited. In: Proceedings of the Fourteenth Italian Conference on Theoretical Computer Science (ICTCS 2013), pp. 200–205 (2013)

    Google Scholar 

  4. Barton, C., Iliopoulos, C.S., Pissis, S.P.: Fast algorithms for approximate circular string matching. Algorithms Mol. Biol. 9(9) (2014)

    Google Scholar 

  5. Barton, C., Iliopoulos, C.S., Kundu, R., Pissis, S.P., Retha, A., Vayani, F.: Accurate and efficient methods to improve multiple circular sequence alignment. In: Bampis, E. (ed.) Experimental Algorithms. Lecture Notes in Computer Science, vol. 9125, pp. 247–258. Springer International Publishing, Cham (2015)

    Google Scholar 

  6. Barton, C., Iliopoulos, C.S., Pissis, S.P.: Average-case optimal approximate circular string matching. In: Dediu, A.H., Formenti, E., Martín-Vide, C., Truthe, B. (eds.) Language and Automata Theory and Applications. Lecture Notes in Computer Science, vol. 8977, pp. 85–96. Springer, Berlin/Heidelberg (2015)

    Google Scholar 

  7. Belazzougui, D.: Succinct dictionary matching with no slowdown. In: Proceedings of the 21st Annual Conference on Combinatorial Pattern Matching, CPM’10, pp. 88–100. Springer, Berlin/Heidelberg (2010)

    Google Scholar 

  8. Chan, H.L., Hon, W.K., Lam, T.W., Sadakane, K.: Compressed indexes for dynamic text collections. ACM Trans. Algorithms 3(2) (2007)

    Google Scholar 

  9. Chen, K.-H., Huang, G.-S., Lee, R.C.-T.: Bit-parallel algorithms for exact circular string matching. Comput. J 57(5), 731–743 (2014)

    Article  Google Scholar 

  10. Crochemore, M., Hancart, C., Lecroq, T.: Algorithms on Strings. Cambridge University Press, New York (2007)

    Book  MATH  Google Scholar 

  11. Dori, S., Landau, G.M.: Construction of Aho Corasick automaton in linear time for integer alphabets. Inf. Process. Lett. 98(2), 66–72 (2006)

    Article  MathSciNet  MATH  Google Scholar 

  12. Ferragina, P., Manzini, G.: Opportunistic data structures with applications. In: Proceedings of the FOCS, pp. 390–398. IEEE Computer Society, Los Alamitos, CA (2000)

    Google Scholar 

  13. Fischer, J.: Inducing the LCP-array. In: Dehne, F., Iacono, J., Sack, J.R. (eds.) Algorithms and Data Structures. Lecture Notes in Computer Science, vol. 6844, pp. 374–385. Springer, Berlin/Heidelberg (2011)

    Chapter  Google Scholar 

  14. Fischer, J., Heun, V.: Space-efficient preprocessing schemes for range minimum queries on static arrays. SIAM J. Comput. 40(2), 465–492 (2011)

    Article  MathSciNet  MATH  Google Scholar 

  15. Fredriksson, K., Grabowski, S.: Average-optimal string matching. J. Discrete Algorithms 7(4), 579–594 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  16. Frousios, K., Iliopoulos, C.S., Mouchard, L., Pissis, S.P., Tischler, G.: REAL: an efficient REad ALigner for next generation sequencing reads. In: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, BCB ’10, pp. 154–159. ACM, New York (2010)

    Google Scholar 

  17. Grossi, R., Iliopoulos, C.S., Mercas, R., Pisanti, N., Pissis, S.P., Retha, A., Vayani, F.: Circular sequence comparison with q-grams. In: Pop, M., Touzet, H. (eds.) Proceedings of Algorithms in Bioinformatics - 15th International Workshop, WABI 2015, Atlanta, GA, Sept 10–12, 2015. Lecture Notes in Computer Science, vol. 9289, pp. 203–216. Springer, Berlin (2015)

    Google Scholar 

  18. Gusfield, D.: Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology. Cambridge University Press, Cambridge (1997)

    Book  MATH  Google Scholar 

  19. Hon, W.K., Ku, T.H., Shah, R., Thankachan, S.V., Vitter, J.S.: Faster compressed dictionary matching. In: Proceedings of the 17th International Conference on String Processing and Information Retrieval, SPIRE’10, pp. 191–200. Springer, Berlin/Heidelberg (2010)

    Google Scholar 

  20. Hon, W.K., Lu, C.H., Shah, R., Thankachan, S.V.: Succinct indexes for circular patterns. In: Proceedings of the 22nd International Conference on Algorithms and Computation, ISAAC’11, pp. 673–682. Springer, Berlin/Heidelberg (2011)

    Google Scholar 

  21. Hon, W.K., Ku, T.H., Shah, R., Thankachan, S.: Space-efficient construction algorithm for the circular suffix tree. In: Fischer, J., Sanders, P. (eds.) Combinatorial Pattern Matching. Lecture Notes in Computer Science, vol. 7922, pp. 142–152. Springer, Berlin/Heidelberg (2013)

    Chapter  Google Scholar 

  22. Huynh, T.N.D., Hon, W.K., Lam, T.W., Sung, W.K.: Approximate string matching using compressed suffix arrays. Theor. Comput. Sci. 352(1–3), 240–249 (2006)

    Article  MathSciNet  MATH  Google Scholar 

  23. Ilie, L., Navarro, G., Tinta, L.: The longest common extension problem revisited and applications to approximate string searching. J. Discrete Algorithms 8(4), 418–428 (2010)

    Article  MathSciNet  MATH  Google Scholar 

  24. Iliopoulos, C.S., Rahman, M.S.: Indexing circular patterns. In: Proceedings of the 2nd International Conference on Algorithms and Computation, WALCOM’08, pp. 46–57. Springer, Berlin/Heidelberg (2008)

    Google Scholar 

  25. Lothaire, M. (ed.): Applied Combinatorics on Words. Cambridge University Press, New York (2005)

    MATH  Google Scholar 

  26. Manber, U., Myers, E.W.: Suffix arrays: a new method for on-line string searches. SIAM J. Comput. 22(5), 935–948 (1993)

    Article  MathSciNet  MATH  Google Scholar 

  27. Nong, G., Zhang, S., Chan, W.H.: Linear suffix array construction by almost pure induced-sorting. In: Proceedings of the 2009 Data Compression Conference, DCC ’09, pp. 193–202. IEEE Computer Society, Washington, DC (2009)

    Google Scholar 

  28. Palazón-González, V., Marzal, A.: Speeding up the cyclic edit distance using LAESA with early abandon. Pattern Recogn. Lett. (2015). http://dx.doi.org/10.1016/j.patrec.2015.04.013

    Google Scholar 

  29. Rivest, R.L.: Partial-match retrieval algorithms. SIAM J. Comput. 5(1), 19–50 (1976). doi:10.1137/0205003

    Article  MathSciNet  MATH  Google Scholar 

  30. Schnattinger, T., Ohlebusch, E., Gog, S.: Bidirectional search in a string with wavelet trees and bidirectional matching statistics. Inf. Comput. 213, 13–22 (2012)

    Article  MathSciNet  MATH  Google Scholar 

  31. Ukkonen, E.: On-line construction of suffix trees. Algorithmica 14(3), 249–260 (1995)

    Article  MathSciNet  MATH  Google Scholar 

  32. Uliel, S., Fliess, A., Unger, R.: Naturally occurring circular permutations in proteins. Protein Eng. 14(8), 533–542 (2001)

    Article  Google Scholar 

  33. Weiner, P.: Linear pattern matching algorithms. In: Proceedings of the 14th Annual Symposium on Switching and Automata Theory (SWAT 1973), pp. 1–11. IEEE Computer Society, Washington, DC (1973)

    Google Scholar 

  34. Wu, S., Manber, U.: Fast text searching: allowing errors. Commun. ACM 35(10), 83–91 (1992)

    Article  Google Scholar 

Download references

Acknowledgements

Part of this research has been supported by an INSPIRE Strategic Partnership Award, administered by the British Council, Bangladesh, for the project titled “Advances in Algorithms for Next Generation Biological Sequences.”

Author information

Authors and Affiliations

  1. Department of Informatics, King’s College London, The Strand, London, WC2R 2LS, UK

    Costas S. Iliopoulos & Solon P. Pissis

  2. AℓEDA Group, Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology (BUET), Dhaka, 1205, Bangladesh

    M. Sohel Rahman

Authors
  1. Costas S. Iliopoulos
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Solon P. Pissis
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. Sohel Rahman
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Solon P. Pissis .

Editor information

Editors and Affiliations

  1. LaTICE, Tunis, Tunisia

    Mourad Elloumi

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this chapter

Cite this chapter

Iliopoulos, C.S., Pissis, S.P., Rahman, M.S. (2017). Searching and Indexing Circular Patterns. In: Elloumi, M. (eds) Algorithms for Next-Generation Sequencing Data. Springer, Cham. https://doi.org/10.1007/978-3-319-59826-0_3

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-59826-0_3

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-59824-6

  • Online ISBN: 978-3-319-59826-0

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation