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Partial Information Network Queries

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Combinatorial Algorithms (IWOCA 2013)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8288))

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Abstract

We present a new pattern matching problem, the partial information query (PIQ) problem, which includes as special cases two problems that have important applications in bioinformatics: the alignment query (AQ) problem and the topology-free query (TFQ) problem. In both problems we have a pattern \(\cal P\) and a graph H, and we seek a subgraph of H that resembles \(\cal P\). AQ requires knowing the topology of \(\cal P\), while TFQ ignores it. PIQ fits the scenario where partial information is available on the topology of \(\cal P\). Our main result is a parameterized algorithm for PIQ, which can handle inputs where \(\cal P\) is a set of trees. It significantly improves the best known running time in solving TFQ. We also improve the best known running times in solving two special cases of AQ.

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References

  1. Alon, N., Yuster, R., Zwick, U.: Color coding. J. Assoc. Comput. Mach. 42(4), 844–856 (1995)

    Article  MathSciNet  MATH  Google Scholar 

  2. Björklund, A., Husfeldt, T., Kaski, P., Koivisto, M.: Narrow sieves for parameterized paths and packings. CoRR abs/1007.1161 (2010)

    Google Scholar 

  3. Blin, G., Sikora, F., Vialette, S.: Querying graphs in protein-protein interactions networks using feedback vertex set. IEEE/ACM Trans. Comput. Biol. Bioinform. 7(4), 628–635 (2010)

    Article  Google Scholar 

  4. Bruckner, S., Hüffner, F., Karp, R.M., Shamir, R., Sharan, R.: Topology-free querying of protein interaction networks. In: Batzoglou, S. (ed.) RECOMB 2009. LNCS, vol. 5541, pp. 74–89. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  5. Chen, J., Kneis, J., Lu, S., Molle, D., Richter, S., Rossmanith, P., Sze, S., Zhang, F.: Randomized divide-and-conquer: Improved path, matching, and packing algorithms. SIAM J. on Computing 38(6), 2526–2547 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  6. Dost, B., Shlomi, T., Gupta, N., Ruppin, E., Bafna, V., Sharan, R.: Qnet: a tool for querying protein interaction networks. J. Comput. Biol. 15(7), 913–925 (2008)

    Article  MathSciNet  Google Scholar 

  7. Downey, R.G., Fellows, M.R.: Fixed-parameter tractability and completeness ii: on completeness for w [1]. Theor. Comput. Sci. 141(1-2), 109–131 (1995)

    Article  MathSciNet  MATH  Google Scholar 

  8. Fionda, V., Palopoli, L.: Biological network querying techniques: Analysis and comparison. J. Comput. Biol. 18(4), 595–625 (2011)

    Article  MathSciNet  Google Scholar 

  9. Garey, M.R., Johnson, D.S.: Computers and intractability: a guide to the theory of NP-completeness. W.H. Freeman, New York (1979)

    MATH  Google Scholar 

  10. Guillemot, S., Sikora, F.: Finding and counting vertex-colored subtrees. In: Hliněný, P., Kučera, A. (eds.) MFCS 2010. LNCS, vol. 6281, pp. 405–416. Springer, Heidelberg (2010)

    Chapter  Google Scholar 

  11. Hüffner, F., Wernicke, S., Zichner, T.: Algorithm engineering for color-coding with applications to signaling pathway detection. Algorithmica 52(2), 114–132 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  12. Koutis, I.: Faster algebraic algorithms for path and packing problems. In: Aceto, L., Damgård, I., Goldberg, L.A., Halldórsson, M.M., Ingólfsdóttir, A., Walukiewicz, I. (eds.) ICALP 2008, Part I. LNCS, vol. 5125, pp. 575–586. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  13. Lacroix, V., Fernandes, C.G., Sagot, M.F.: Motif search in graphs: Application to metabolic networks. IEEE/ACM Trans. Comput. Biol. Bioinform. 3(4), 360–368 (2006)

    Article  Google Scholar 

  14. Mano, A., Tuller, T., Beja, O., Pinter, R.Y.: Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways. BMC Bioinform 11(S-1), S38 (2010)

    Google Scholar 

  15. Niedermeier, R.: Invitation to fixed-parameter algorithms. Oxford University Press (2006)

    Google Scholar 

  16. Pinter, R.Y., Rokhlenko, O., Tsur, D., Ziv-Ukelson, M.: Approximate labelled subtree homeomorphism. J. Discrete Algorithms 6(3), 480–496 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  17. Pinter, R.Y., Rokhlenko, O., Yeger-Lotem, E., Ziv-Ukelson, M.: Alignment of metabolic pathways. Bioinformatics 21(16), 3401–3408 (2005)

    Article  Google Scholar 

  18. Pinter, R.Y., Zehavi, M.: Algorithms for topology-free and alignment queries. Technion Technical Reports CS-2012-12 (2012)

    Google Scholar 

  19. Shlomi, T., Segal, D., Ruppin, E., Sharan, R.: Qpath: a method for querying pathways in a protein-protein interaction networks. BMC Bioinform. 7, 199 (2006)

    Article  Google Scholar 

  20. Sikora, F.: An (almost complete) state of the art around the graph motif problem. Université Paris-Est Technical reports (2012)

    Google Scholar 

  21. Wang, H., Xiang, T., Hu, X.: Research on pattern matching with wildcards and length constraints: methods and completeness (2012), http://www.intechopen.com/books/bioinformatics

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Authors and Affiliations

  1. Department of Computer Science, Technion - Israel Institute of Technology, Haifa, 32000, Israel

    Ron Y. Pinter & Meirav Zehavi

Authors
  1. Ron Y. Pinter
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  2. Meirav Zehavi
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Editors and Affiliations

  1. UFR des Sciences et Techniques, LITIS, Université de Rouen, 76821, EA 4180, Mont Saint Aignan Cedex, France

    Thierry Lecroq  & Laurent Mouchard  & 

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Pinter, R.Y., Zehavi, M. (2013). Partial Information Network Queries. In: Lecroq, T., Mouchard, L. (eds) Combinatorial Algorithms. IWOCA 2013. Lecture Notes in Computer Science, vol 8288. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-45278-9_31

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  • DOI: https://doi.org/10.1007/978-3-642-45278-9_31

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-45277-2

  • Online ISBN: 978-3-642-45278-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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