Skip to main content

Reversal Distances for Strings with Few Blocks or Small Alphabets

  • Conference paper
Combinatorial Pattern Matching (CPM 2014)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8486))

Included in the following conference series:

Abstract

We study the String Reversal Distance problem, an extension of the well-known Sorting by Reversals problem. String Reversal Distance takes two strings S and T as input, and asks for a minimum number of reversals to obtain T from S. We consider four variants: String Reversal Distance, String Prefix Reversal Distance (in which any reversal must include the first letter of the string), and the signed variants of these problems, namely Signed String Reversal Distance and Signed String Prefix Reversal Distance. We study algorithmic properties of these four problems, in connection with two parameters of the input strings: the number of blocks they contain (a block being maximal substring such that all letters in the substring are equal), and the alphabet size Σ. For instance, we show that Signed String Reversal Distance and Signed String Prefix Reversal Distance are NP-hard even if the input strings have only one letter.

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

Access this chapter

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 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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Bafna, V., Pevzner, P.A.: Genome rearrangements and sorting by reversals. SIAM J. Comput. 25(2), 272–289 (1996)

    Article  MATH  MathSciNet  Google Scholar 

  2. Berman, P., Hannenhalli, S., Karpinski, M.: 1.375-approximation algorithm for sorting by reversals. In: Möhring, R.H., Raman, R. (eds.) ESA 2002. LNCS, vol. 2461, pp. 200–210. Springer, Heidelberg (2002)

    Chapter  Google Scholar 

  3. Bulteau, L., Fertin, G., Rusu, I.: Pancake flipping is hard. In: Rovan, B., Sassone, V., Widmayer, P. (eds.) MFCS 2012. LNCS, vol. 7464, pp. 247–258. Springer, Heidelberg (2012)

    Chapter  Google Scholar 

  4. Caprara, A.: Sorting by reversals is difficult. In: Proc. 1st RECOMB, pp. 75–83 (1997)

    Google Scholar 

  5. Chen, X., Zheng, J., Fu, Z., Nan, P., Zhong, Y., Lonardi, S., Jiang, T.: Assignment of orthologous genes via genome rearrangement. IEEE ACM T. Comput. Bi. 2(4), 302–315 (2005)

    Google Scholar 

  6. Christie, D.A.: Genome Rearrangement Problems. PhD thesis, University of Glasgow (1998)

    Google Scholar 

  7. Christie, D.A., Irving, R.W.: Sorting strings by reversals and by transpositions. SIAM J. Discrete Math. 14(2), 193–206 (2001)

    Article  MATH  MathSciNet  Google Scholar 

  8. Fertin, G., Labarre, A., Rusu, I., Tannier, E., Vialette, S.: Combinatorics of Genome Rearrangements. Computational Molecular Biology. MIT Press (2009)

    Google Scholar 

  9. Fischer, J., Ginzinger, S.W.: A 2-approximation algorithm for sorting by prefix reversals. In: Brodal, G.S., Leonardi, S. (eds.) ESA 2005. LNCS, vol. 3669, pp. 415–425. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  10. Fu, Z., Chen, X., Vacic, V., Nan, P., Zhong, Y., Jiang, T.: MSOAR: A high-throughput ortholog assignment system based on genome rearrangement. J. Comput. Biol. 14(9), 1160–1175 (2007)

    Article  MathSciNet  Google Scholar 

  11. Hurkens, C.A.J., van Iersel, L., Keijsper, J., Kelk, S., Stougie, L., Tromp, J.: Prefix reversals on binary and ternary strings. SIAM J. Discrete Math. 21(3), 592–611 (2007)

    Article  MATH  MathSciNet  Google Scholar 

  12. Jiang, T.: Some algorithmic challenges in genome-wide ortholog assignment. J. Comput. Sci. Technol. 25(1), 42–52 (2010)

    Article  Google Scholar 

  13. Radcliffe, A., Scott, A., Wilmer, E.: Reversals and transpositions over finite alphabets. SIAM J. Discrete Math. 19(1), 224 (2006)

    Article  MathSciNet  Google Scholar 

  14. Watterson, G., Ewens, W., Hall, T., Morgan, A.: The chromosome inversion problem. J. Theor. Biol. 99(1), 1–7 (1982)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer International Publishing Switzerland

About this paper

Cite this paper

Bulteau, L., Fertin, G., Komusiewicz, C. (2014). Reversal Distances for Strings with Few Blocks or Small Alphabets. In: Kulikov, A.S., Kuznetsov, S.O., Pevzner, P. (eds) Combinatorial Pattern Matching. CPM 2014. Lecture Notes in Computer Science, vol 8486. Springer, Cham. https://doi.org/10.1007/978-3-319-07566-2_6

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-07566-2_6

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-07565-5

  • Online ISBN: 978-3-319-07566-2

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics