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International Conference on Current Trends in Theory and Practice of Computer Science

SOFSEM 2007: SOFSEM 2007: Theory and Practice of Computer Science pp 465–474Cite as

Indexing Factors with Gaps

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4362))

Abstract

Indexing of factors is a widely used and useful technique in stringology and can be seen as a tool in solving diverse text algorithmic problems. A gapped-factor is a concatenation of a factor of length k, a gap of length d and another factor of length k′. The problem of indexing the gapped-factors was considered recently by [18]. In this paper, we present a new improved indexing scheme for the gapped-factors.

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References

  1. Agarwal, P.K., Govindarajan, S., Muthukrishnan, S.: Range Searching in Categorical Data: Colored Range Searching on Grid. In: Möhring, R.H., Raman, R. (eds.) ESA 2002. LNCS, vol. 2461, pp. 17–28. Springer, Heidelberg (2002)

    Chapter  Google Scholar 

  2. Allali, J., Sagot, M.-F.: The at Most k-Deep Factor Tree. Technical Report 2004-03 (2004)

    Google Scholar 

  3. Alstrup, S., Brodal, G.S., Rauhe, T.: New Data Structures for Orthogonal Range Searching. In: FOCS, pp. 198–207 (2000)

    Google Scholar 

  4. Brudno, M., Chapman, M., Göttgens, B., Batzoglou, S., Morgenstern, B.: Fast and Sensitive Multiple Alignment of Large Genomic Sequences. BMC Bioinformatics 4, 66 (2003)

    Article  Google Scholar 

  5. Brudno, M., Do, C.B., Cooper, G.M., Kim, M.F., Davydov, E., Green, E.D., Sidow, A., Batzoglou, S.: Lagan and Multi-Lagan: Efficient Tools for Large-Scale Multiple Alignment of Genomic Dna. Genome Research 13(4), 721–731 (2003)

    Article  Google Scholar 

  6. Crochemore, M., Rytter, W.: Jewels of Stringology. World Scientific, Singapore (2002)

    Google Scholar 

  7. Edgar, R.C.: Muscle: Multiple Sequence Alignment with High Accuracy and High Throughput. Nucleic Acids Research 32(5), 1792–1797 (2004)

    Article  Google Scholar 

  8. Gravano, L., Ipeirotis, P.G., Jagadish, H.V., Koudas, N., Muthukrishnan, S., Srivastava, D.: Approximate String Joins in a Database (almost) for Free. In: Apers, P.M.G., Atzeni, P., Ceri, S., Paraboschi, S., Ramamohanarao, K., Snodgrass, R.T. (eds.) VLDB, pp. 491–500. Morgan Kaufmann, San Francisco (2001)

    Google Scholar 

  9. Gusfield, D.: Algorithms on Strings, Trees, and Sequences – Computer Science and Computational Biology. Cambridge University Press, Cambridge (1997)

    MATH  Google Scholar 

  10. Höhl, M., Kurtz, S., Ohlebusch, E.: Efficient Multiple Genome Alignment. In: ISMB, pp. 312–320 (2002)

    Google Scholar 

  11. Iliopoulos, C.S., McHugh, J.A.M., Peterlongo, P.: A First Approach to Finding Common Motifs with Gaps. J. Found. Comput. Sci. 16(6), 1145–1154 (2005)

    Article  MATH  MathSciNet  Google Scholar 

  12. Li, M., Ma, B., Kisman, D., Tromp, J.: Patternhunter ii: Highly Sensitive and Fast Homology Search. Genome Informatics 14, 164–175 (2003)

    Google Scholar 

  13. Ma, B., Tromp, J., Li, M.: Patternhunter: Faster and More Sensitive Homology Search. Bioinformatics 18(3), 440–445 (2002)

    Article  Google Scholar 

  14. McCreight, E.M.: A Space-Economical Suffix Tree Construction Algorithm. J. ACM 23(2), 262–272 (1976)

    Article  MATH  MathSciNet  Google Scholar 

  15. Michael, M., Dieterich, C., Vingron, M.: Siteblast-Rapid and Sensitive Local Alignment of Genomic Sequences Employing Motif Anchors. Bioinformatics 21(9), 2093–2094 (2005)

    Article  Google Scholar 

  16. Muthukrishnan, S.: Efficient Algorithms for Document Retrieval Problems. In: SODA, pp. 657–666 (2002)

    Google Scholar 

  17. Navarro, G., Sutinen, E., Tanninen, J., Tarhio, J.: Indexing Text with Approximate q-Grams. In: Giancarlo, R., Sankoff, D. (eds.) CPM 2000. LNCS, vol. 1848, pp. 350–363. Springer, Heidelberg (2000)

    Chapter  Google Scholar 

  18. Peterlongo, P., Allali, J., Sagot, M.-F.: The Gapped-Factor Tree. In: The Prague Stringology Conference, to appear (2006)

    Google Scholar 

  19. Sutinen, E., Tarhio, J.: On Using q-Gram Locations in Approximate String Matching. In: Spirakis, P.G. (ed.) ESA 1995. LNCS, vol. 979, pp. 327–340. Springer, Heidelberg (1995)

    Google Scholar 

  20. Ukkonen, E.: On-Line Construction of Suffix Trees. Algorithmica 14(3), 249–260 (1995)

    Article  MATH  MathSciNet  Google Scholar 

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Author information

Authors and Affiliations

  1. Algorithm Design Group, Department of Computer Science, King’s College London, Strand, London WC2R 2LS, England

    M. Sohel Rahman & Costas S. Iliopoulos

Authors
  1. M. Sohel Rahman
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  2. Costas S. Iliopoulos
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Editor information

Jan van Leeuwen Giuseppe F. Italiano Wiebe van der Hoek Christoph Meinel Harald Sack František Plášil

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Rahman, M.S., Iliopoulos, C.S. (2007). Indexing Factors with Gaps. In: van Leeuwen, J., Italiano, G.F., van der Hoek, W., Meinel, C., Sack, H., Plášil, F. (eds) SOFSEM 2007: Theory and Practice of Computer Science. SOFSEM 2007. Lecture Notes in Computer Science, vol 4362. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69507-3_40

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  • DOI: https://doi.org/10.1007/978-3-540-69507-3_40

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-69506-6

  • Online ISBN: 978-3-540-69507-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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