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.
Keywords
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Alon, N., Yuster, R., Zwick, U.: Color coding. J. Assoc. Comput. Mach. 42(4), 844–856 (1995)
Björklund, A., Husfeldt, T., Kaski, P., Koivisto, M.: Narrow sieves for parameterized paths and packings. CoRR abs/1007.1161 (2010)
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)
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)
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)
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)
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)
Fionda, V., Palopoli, L.: Biological network querying techniques: Analysis and comparison. J. Comput. Biol. 18(4), 595–625 (2011)
Garey, M.R., Johnson, D.S.: Computers and intractability: a guide to the theory of NP-completeness. W.H. Freeman, New York (1979)
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)
Hüffner, F., Wernicke, S., Zichner, T.: Algorithm engineering for color-coding with applications to signaling pathway detection. Algorithmica 52(2), 114–132 (2008)
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)
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)
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)
Niedermeier, R.: Invitation to fixed-parameter algorithms. Oxford University Press (2006)
Pinter, R.Y., Rokhlenko, O., Tsur, D., Ziv-Ukelson, M.: Approximate labelled subtree homeomorphism. J. Discrete Algorithms 6(3), 480–496 (2008)
Pinter, R.Y., Rokhlenko, O., Yeger-Lotem, E., Ziv-Ukelson, M.: Alignment of metabolic pathways. Bioinformatics 21(16), 3401–3408 (2005)
Pinter, R.Y., Zehavi, M.: Algorithms for topology-free and alignment queries. Technion Technical Reports CS-2012-12 (2012)
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)
Sikora, F.: An (almost complete) state of the art around the graph motif problem. Université Paris-Est Technical reports (2012)
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
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
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
Download citation
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)