Skip to main content

Revisiting T. Uno and M. Yagiura’s Algorithm

  • Conference paper
Algorithms and Computation (ISAAC 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3827))

Included in the following conference series:

Abstract

In 2000, T. Uno and M. Yagiura published an algorithm that computes all the K common intervals of two given permutations of length n in \(\mathcal{O}(n+ K)\) time. Our paper first presents a decomposition approach to obtain a compact encoding for common intervals of d permutations. Then, we revisit T. Uno and M. Yagiura’s algorithm to yield a linear time algorithm for finding this encoding. Besides, we adapt the algorithm to obtain a linear time modular decomposition of an undirected graph, and thereby propose a formal invariant-based proof for all these algorithms.

Full version available at http://www.lirmm.fr/~buixuan as RR-LIRMM-05049

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 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever

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. Béal, M.-P., Bergeron, A., Corteel, S., Raffinot, M.: An algorithmic view of gene teams. Theoretical Computer Science 320(2-3), 395–418 (2004)

    Article  MATH  MathSciNet  Google Scholar 

  2. Bérard, S., Bergeron, A., Chauve, C.: Conservation of combinatorial structures in evolution scenarios. In: Lagergren, J. (ed.) RECOMB-WS 2004. LNCS (LNBI), vol. 3388, pp. 1–14. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  3. Bergeron, A., Chauve, C., de Montgolfier, F., Raffinot, M.: Computing common intervals of k permutations, with applications to modular decomposition of graphs. In: Brodal, G.S., Leonardi, S. (eds.) ESA 2005. LNCS, vol. 3669, pp. 779–790. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  4. Bergeron, A., Stoye, J.: On the similarity of sets of permutations and its applications to genome comparison. In: Warnow, T.J., Zhu, B. (eds.) COCOON 2003. LNCS, vol. 2697, pp. 68–79. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  5. Bogart, K.P., Fishburn, P.C., Isaak, G., Langley, L.: Proper and unit tolerance graphs. Discrete Applied Mathematics 60, 99–117 (1995)

    Article  MATH  MathSciNet  Google Scholar 

  6. Capelle, C.: Block decomposition of inheritance hierarchies. In: Möhring, R.H. (ed.) WG 1997. LNCS, vol. 1335, pp. 118–131. Springer, Heidelberg (1997)

    Chapter  Google Scholar 

  7. Capelle, C., Habib, M., de Montgolfier, F.: Graph decomposition and factorizing permutations. Discrete Mathematics and Theoretical Computer Science 5(1), 55–70 (2002)

    MATH  MathSciNet  Google Scholar 

  8. Chein, M., Habib, M., Maurer, M.C.: Partitive hypergraphs. Discrete Mathematics 37(1), 35–50 (1981)

    Article  MATH  MathSciNet  Google Scholar 

  9. Cournier, A., Habib, M.: A new linear algorithm for modular decomposition. In: Tison, S. (ed.) CAAP 1994. LNCS, vol. 787, pp. 68–84. Springer, Heidelberg (1994)

    Chapter  Google Scholar 

  10. Dahlhaus, E.: Parallel algorithms for hierarchical clustering, and applications to split decomposition and parity graph recognition. Journal of Algorithms 36(2), 205–240 (2000)

    Article  MATH  MathSciNet  Google Scholar 

  11. de Berg, M., van Kreveld, M., Overmars, M., Schwarzkopf, O.: Computational geometry. Springer, Heidelberg (1991)

    Google Scholar 

  12. de Montgolfier, F.: Décomposition modulaire des graphes. Théorie, extensions et algorithmes. PhD thesis, Université Montpellier II (2003)

    Google Scholar 

  13. Felsner, S.: Tolerance graphs and orders. Journal of Graph Theory 28(3), 129–140 (1998)

    Article  MATH  MathSciNet  Google Scholar 

  14. Figeac, M., Varré, J.-S.: Sorting by reversals with common intervals. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), vol. 3240, pp. 26–37. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  15. Habib, M., de Montgolfier, F., Paul, C.: A simple linear-time modular decomposition algorithm. In: Hagerup, T., Katajainen, J. (eds.) SWAT 2004. LNCS, vol. 3111, pp. 187–198. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  16. Habib, M., Huchard, M., Spinrad, J.P.: A linear algorithm to decompose inheritance graphs into modules. Algorithmica 13(6), 573–591 (1995)

    Article  MATH  MathSciNet  Google Scholar 

  17. Heber, S., Stoye, J.: Finding all common intervals of k permutations. In: Amir, A., Landau, G.M. (eds.) CPM 2001. LNCS, vol. 2089, pp. 207–218. Springer, Heidelberg (2001)

    Chapter  Google Scholar 

  18. Hsu, W.-L., Ma, T.-M.: Substitution decomposition on chordal graphs and applications. In: Hsu, W.-L., Lee, R.C.T. (eds.) ISA 1991. LNCS, vol. 557, pp. 52–60. Springer, Heidelberg (1991)

    Google Scholar 

  19. Landau, G.M., Parida, L., Weimann, O.: Using pq trees for comparative genomics. In: Apostolico, A., Crochemore, M., Park, K. (eds.) CPM 2005. LNCS, vol. 3537, pp. 128–143. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  20. McConnell, R.M., de Montgolfier, F.: Algebraic Operations on PQ Trees and Modular Decomposition Trees. In: Kratsch, D. (ed.) WG 2005. LNCS, vol. 3787, pp. 421–432. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  21. McConnell, R.M., Spinrad, J.P.: Modular decomposition and transitive orientation. Discrete Mathematics 201, 189–241 (1999)

    Article  MATH  MathSciNet  Google Scholar 

  22. Möhring, R.H., Radermacher, F.J.: Substitution decomposition for discrete structures and connections with combinatorial optimization. Annals of Discrete Mathematics 19, 257–356 (1984)

    Google Scholar 

  23. Uno, T., Yagiura, M.: Fast algorithms to enumerate all common intervals of two permutations. Algorithmica 26(2), 290–309 (2000)

    Article  MATH  MathSciNet  Google Scholar 

  24. Welsh, D.J.A.: Matroids: Fundamental concepts. In: Handbook of Combinatorics, vol. 1, pp. 481–526. North-Holland, Amsterdam (1995)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Xuan, BM.B., Habib, M., Paul, C. (2005). Revisiting T. Uno and M. Yagiura’s Algorithm. In: Deng, X., Du, DZ. (eds) Algorithms and Computation. ISAAC 2005. Lecture Notes in Computer Science, vol 3827. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11602613_16

Download citation

  • DOI: https://doi.org/10.1007/11602613_16

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-30935-2

  • Online ISBN: 978-3-540-32426-3

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics