Abstract
This work deals with the program Structator — a fast index-based search tool for RNA sequence-structure patterns. We present two space efficient modifications which both outperform the existing methods when searching large databases. Thus, our new methods make the program accessible for a wider range of real-world applications.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Abouelhoda, M.I., Kurtz, S., Ohlebusch, E.: Replacing suffix trees with enhanced suffix arrays. J. Discrete Algorithm 2, 53–86 (2004)
Beckstette, M., Homann, R., Giegerich, R., Kurtz, S.: Fast index based algorithms and software for matching position specific scoring matrices. BMC Bioinformatics 7, 389 (2006)
Fischer, J.: Combined Data Structure for Previous- and Next-Smaller-Values. Theor. Comput. Sci. 412(22), 2451–2456 (2011)
Fischer, J., Heun, V.: Space-Efficient Preprocessing Schemes for Range Minimum Queries on Static Arrays. SIAM J. Comput. 40(2), 465–492 (2011)
Gardner, P.P., Wilm, A., Washietl, S.: A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res. 33, 2433–2439 (2005)
Gardner, P.P., Daub, J., Tate, J., Moore, B.L., Osuch, I.H., Griffiths-Jones, S., Finn, R.D., Nawrocki, E.P., Kolbe, D.L., Eddy, S.R., Bateman, A.: Rfam: Wikipedia, clans and the ”decimal” release. Nucleic Acids Res. 39, D141–D145 (2011)
Kärkkäinen, J., Sanders, P.: Simple Linear Work Suffix Array Construction. In: Baeten, J.C.M., Lenstra, J.K., Parrow, J., Woeginger, G.J. (eds.) ICALP 2003. LNCS, vol. 2719, pp. 943–955. Springer, Heidelberg (2003)
Kasai, T., Lee, G., Arimura, H., Arikawa, S., Park, K.: Linear-Time Longest-Common-Prefix Computation in Suffix Arrays and Its Applications. In: Amir, A., Landau, G.M. (eds.) CPM 2001. LNCS, vol. 2089, pp. 181–192. Springer, Heidelberg (2001)
Kim, D.-K., Sim, J.S., Park, H.-J., Park, K.: Linear-Time Construction of Suffix Arrays. In: Baeza-Yates, R., Chávez, E., Crochemore, M. (eds.) CPM 2003. LNCS, vol. 2676, pp. 186–199. Springer, Heidelberg (2003)
Ko, P., Aluru, S.: Space Efficient Linear Time Construction of Suffix Arrays. In: Baeza-Yates, R., Chávez, E., Crochemore, M. (eds.) CPM 2003. LNCS, vol. 2676, pp. 200–210. Springer, Heidelberg (2003)
Mattick, J.S.: RNA regulation: a new genetics? Nat. Rev. Genet. 5, 316–323 (2004)
Mattick, J.S., Taft, R.J., Faulkner, G.J.: A global view of genomic information-moving beyond the gene and the master regulator. Trends Genet. 26, 21–28 (2010)
Meyer, F., Kurtz, S., Backofen, R., Will, S., Beckstette, M.: Structator: fast index-based search for RNA sequence-structure patterns. BMC Bioinformatics 12, 214 (2011)
Myers, U., Manber, G.: Suffix arrays: a new method for on-line string searches. SIAM J. Comput. 22, 935–948 (1993)
Strothmann, D.: The affix array data structure and its applications to RNA secondary structure analysis. Theor. Comput. Sci. 389(1-2), 278–294 (2007)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Albrecht, B., Heun, V. (2012). Space Efficient Modifications to Structator— A Fast Index-Based Search Tool for RNA Sequence-Structure Patterns. In: Klasing, R. (eds) Experimental Algorithms. SEA 2012. Lecture Notes in Computer Science, vol 7276. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30850-5_4
Download citation
DOI: https://doi.org/10.1007/978-3-642-30850-5_4
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-30849-9
Online ISBN: 978-3-642-30850-5
eBook Packages: Computer ScienceComputer Science (R0)