Skip to main content
SpringerLink
Log in

The Colored Longest Common Prefix Array Computed via Sequential Scans

  • Conference paper
  • First Online:
String Processing and Information Retrieval (SPIRE 2018)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 11147))

Included in the following conference series:

Abstract

Due to the increased availability of large datasets of biological sequences, tools for sequence comparison are now relying on efficient alignment-free approaches to a greater extent. Most alignment-free approaches require the computation of statistics when comparing sequences, even if such computations may not scale well in in internal memory when very large collections of long sequences are considered. In this paper, we present a new conceptual data structure, the colored longest common prefix array (cLCP), that allows to efficiently tackle several problems with an alignment-free approach. In fact, we show that such a data structure can be computed via sequential scans in semi-external memory. By using cLCP, we propose an efficient lightweight strategy to solve the multi-string Average Common Substring (ACS) problem, that consists in the pairwise comparison of a single string against a collection of m strings simultaneously, in order to obtain m ACS induced distances. Experimental results confirm the high practical efficiency of our approach.

G.R. and M.S. are partially supported and D.V. is supported by the project Italian MIUR-SIR CMACBioSeq (“Combinatorial methods for analysis and compression of biological sequences”) grant n. RBSI146R5L.

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 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight 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. https://github.com/giovannarosone/cLCP-mACS

  2. https://github.com/BEETL/BEETL

  3. https://github.com/giovannarosone/BCR_LCP_GSA

  4. https://github.com/felipelouza/egsa

  5. https://github.com/felipelouza/egap

  6. http://kmacs.gobics.de/

  7. Apostolico, A., Guerra, C., Pizzi, C.: Alignment free sequence similarity with bounded hamming distance. In: Data Compression Conference, DCC 2014, pp. 183–192. IEEE (2014)

    Google Scholar 

  8. Bauer, M., Cox, A., Rosone, G.: Lightweight algorithms for constructing and inverting the BWT of string collections. Theor. Comput. Sci. 483, 134–148 (2013)

    Article  MathSciNet  Google Scholar 

  9. Belazzougui, D., Cunial, F.: Indexed matching statistics and shortest unique substrings. In: Moura, E., Crochemore, M. (eds.) SPIRE 2014. LNCS, vol. 8799, pp. 179–190. Springer, Cham (2014). https://doi.org/10.1007/978-3-319-11918-2_18

    Chapter  Google Scholar 

  10. Belazzougui, D., Cunial, F.: Fast label extraction in the CDAWG. In: Fici, G., Sciortino, M., Venturini, R. (eds.) SPIRE 2017. LNCS, vol. 10508, pp. 161–175. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-67428-5_14

    Chapter  MATH  Google Scholar 

  11. Burrows, M., Wheeler, D.: A block sorting data compression algorithm. Technical report, DEC Systems Research Center (1994)

    Google Scholar 

  12. Chang, W.I., Lawler, E.L.: Sublinear approximate string matching and biological applications. Algorithmica 12(4), 327–344 (1994)

    Article  MathSciNet  Google Scholar 

  13. Cohen, E., Chor, B.: Detecting phylogenetic signals in eukaryotic whole genome sequences. J. Comput. Biol. 19(8), 945–956 (2012)

    Article  MathSciNet  Google Scholar 

  14. Comin, M., Verzotto, D.: The irredundant class method for remote homology detection of protein sequences. J. Comput. Biol. 18(12), 1819–1829 (2011)

    Article  Google Scholar 

  15. Comin, M., Verzotto, D.: Alignment-free phylogeny of whole genomes using underlying subwords. Algorithms Mol. Biol. 7(1), 34 (2012)

    Article  Google Scholar 

  16. Comin, M., Verzotto, D.: Whole-genome phylogeny by virtue of unic subwords. In: DEXA, pp. 190–194. IEEE (2012)

    Google Scholar 

  17. Comin, M., Verzotto, D.: Comparing, ranking and filtering motifs with character classes: application to biological sequences analysis. In: Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, chap. 13. Wiley (2013)

    Google Scholar 

  18. Comin, M., Verzotto, D.: Filtering degenerate patterns with application to protein sequence analysis. Algorithms 6(2), 352–370 (2013)

    Article  MathSciNet  Google Scholar 

  19. Comin, M., Verzotto, D.: Beyond fixed-resolution alignment-free measures for mammalian enhancers sequence comparison. IEEE/ACM Trans. Comput. Biol. Bioinform. 11(4), 628–637 (2014)

    Article  Google Scholar 

  20. Cox, A.J., Garofalo, F., Rosone, G., Sciortino, M.: Lightweight LCP construction for very large collections of strings. J. Discret. Algorithms 37, 17–33 (2016)

    Article  MathSciNet  Google Scholar 

  21. Cox, A.J., Jakobi, T., Rosone, G., Schulz-Trieglaff, O.B.: Comparing DNA sequence collections by direct comparison of compressed text indexes. In: Raphael, B., Tang, J. (eds.) WABI 2012. LNCS, vol. 7534, pp. 214–224. Springer, Heidelberg (2012). https://doi.org/10.1007/978-3-642-33122-0_17

    Chapter  Google Scholar 

  22. Egidi, L., Louza, F.A., Manzini, G., Telles, G.P.: External memory BWT and LCP computation for sequence collections with applications. ArXiv e-prints (2018)

    Google Scholar 

  23. Ferraro Petrillo, U., Guerra, C., Pizzi, C.: A new distributed alignment-free approach to compare whole proteomes. Theor. Comput. Sci. 698, 100–112 (2017)

    Article  MathSciNet  Google Scholar 

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

    Book  Google Scholar 

  25. Leimeister, C.A., Morgenstern, B.: Kmacs: the k-mismatch average common substring approach to alignment-free sequence comparison. Bioinformatics 30(14), 2000–2008 (2014)

    Article  Google Scholar 

  26. Louza, F., Telles, G., Hoffmann, S., Ciferri, C.: Generalized enhanced suffix array construction in external memory. Algorithms Mol. Biol. 12(1), 26 (2017)

    Article  Google Scholar 

  27. Manber, U., Myers, G.: Suffix arrays: a new method for on-line string searches. In: Proceedings of the First Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 1990, pp. 319–327. Society for Industrial and Applied Mathematics (1990)

    Google Scholar 

  28. Mantaci, S., Restivo, A., Rosone, G., Sciortino, M.: An extension of the Burrows-Wheeler transform. Theor. Comput. Sci. 387(3), 298–312 (2007)

    Article  MathSciNet  Google Scholar 

  29. Mantaci, S., Restivo, A., Rosone, G., Sciortino, M.: A new combinatorial approach to sequence comparison. Theory Comput. Syst. 42(3), 411–429 (2008)

    Article  MathSciNet  Google Scholar 

  30. Ohlebusch, E., Gog, S., Kügel, A.: Computing matching statistics and maximal exact matches on compressed full-text indexes. In: Chavez, E., Lonardi, S. (eds.) SPIRE 2010. LNCS, vol. 6393, pp. 347–358. Springer, Heidelberg (2010). https://doi.org/10.1007/978-3-642-16321-0_36

    Chapter  Google Scholar 

  31. Pizzi, C.: MissMax: alignment-free sequence comparison with mismatches through filtering and heuristics. Algorithms Mol. Biol. 11, 6 (2016)

    Article  Google Scholar 

  32. Puglisi, S.J., Turpin, A.: Space-time tradeoffs for longest-common-prefix array computation. In: Hong, S.-H., Nagamochi, H., Fukunaga, T. (eds.) ISAAC 2008. LNCS, vol. 5369, pp. 124–135. Springer, Heidelberg (2008). https://doi.org/10.1007/978-3-540-92182-0_14

    Chapter  MATH  Google Scholar 

  33. Ren, J., Song, K., Sun, F., Deng, M., Reinert, G.: Multiple alignment-free sequence comparison. Bioinformatics 29(21), 2690–2698 (2013)

    Article  Google Scholar 

  34. Sadakane, K.: Compressed suffix trees with full functionality. Theory Comput. Syst. 41(4), 589–607 (2007)

    Article  MathSciNet  Google Scholar 

  35. Thankachan, S., Chockalingam, S., Liu, Y., Apostolico, A., Aluru, S.: ALFRED: a practical method for alignment-free distance computation. J. Comput. Biol. 23(6), 452–460 (2016)

    Article  MathSciNet  Google Scholar 

  36. Ulitsky, I., Burstein, D., Tuller, T., Chor, B.: The average common substring approach to phylogenomic reconstruction. J. Comput. Biol. 13(2), 336–350 (2006)

    Article  MathSciNet  Google Scholar 

  37. Zielezinski, A., Vinga, S., Almeida, J., Karlowski, W.: Alignment-free sequence comparison: benefits, applications, and tools. Genome Biol. 18(1), 186 (2017)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. University of Palermo, Palermo, Italy

    Fabio Garofalo & Marinella Sciortino

  2. University of Pisa, Pisa, Italy

    Giovanna Rosone & Davide Verzotto

Authors
  1. Fabio Garofalo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Giovanna Rosone
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Marinella Sciortino
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Davide Verzotto
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Giovanna Rosone .

Editor information

Editors and Affiliations

  1. Diego Portales University, Santiago, Chile

    Travis Gagie

  2. The University of Melbourne, Melbourne, VIC, Australia

    Alistair Moffat

  3. University of Chile, Santiago, Chile

    Gonzalo Navarro

  4. Universidad de Ingeniería y Tecnología, Lima, Peru

    Ernesto Cuadros-Vargas

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Garofalo, F., Rosone, G., Sciortino, M., Verzotto, D. (2018). The Colored Longest Common Prefix Array Computed via Sequential Scans. In: Gagie, T., Moffat, A., Navarro, G., Cuadros-Vargas, E. (eds) String Processing and Information Retrieval. SPIRE 2018. Lecture Notes in Computer Science(), vol 11147. Springer, Cham. https://doi.org/10.1007/978-3-030-00479-8_13

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-00479-8_13

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-00478-1

  • Online ISBN: 978-3-030-00479-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation