Skip to main content

Prefix-Shuffled Geometric Suffix Tree

  • Conference paper
String Processing and Information Retrieval (SPIRE 2007)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4726))

Included in the following conference series:


Protein structure analysis is one of the most important research issues in the post-genomic era, and faster and more accurate index data structures for such 3-D structures are highly desired for research on proteins. The geometric suffix tree is a very sophisticated index structure that enables fast and accurate search on protein 3-D structures. By using it, we can search from 3-D structure databases for all the substructures whose RMSDs (root mean square deviations) to a given query 3-D structure are not larger than a given bound. In this paper, we propose a new data structure based on the geometric suffix tree whose query performance is much better than the original geometric suffix tree. We call the modified data structure the prefix-shuffled geometric suffix tree (or PSGST for short). According to our experiments, the PSGST outperforms the geometric suffix tree in most cases. The PSGST shows its best performance when the database does not have many substructures similar to the query. The query is sometimes 100 times faster than the original geometric suffix trees in such cases.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others


  1. Arun, K.S., Huang, T.S., Blostein, S.D.: Least-squares fitting of two 3-D point sets. IEEE Trans Pattern Anal. Machine Intell. 9, 698–700 (1987)

    Article  Google Scholar 

  2. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The protein data bank. Nucl. Acids Res. 28, 235–242 (2000)

    Article  Google Scholar 

  3. Cormen, T.H., Leiserson, C.E., Rivest, R.L.: Introduction to Algorithms, 2nd edn. MIT Press, Cambridge (2001)

    MATH  Google Scholar 

  4. Eggert, D.W., Lorusso, A., Fisher, R.B.: Estimating 3-D rigid body transformations: a comparison of four major algorithms. Machine Vision and Applications 9, 272–290 (1997)

    Article  Google Scholar 

  5. Eidhammer, I., Jonassen, I., Taylor, W.R.: Structure Comparison and Structure Patterns. J. Computational Biology 7(5), 685–716 (2000)

    Article  Google Scholar 

  6. Farach, M.: Optimal suffix tree construction with large alphabets. In: Proc. 38th IEEE Symp. Foundations of Computer Science, pp. 137–143. IEEE Computer Society Press, Los Alamitos (1997)

    Chapter  Google Scholar 

  7. Golub, G.H., Van Loan, C.F.: Matrix Computation, 3rd edn. John Hopkins University Press (1996)

    Google Scholar 

  8. Gusfield, D.: Algorithms on strings, trees, and sequences: computer science and computational biology. Cambridge University Press, Cambridge (1997)

    MATH  Google Scholar 

  9. Matsumoto, M., Nishimura, T.: A nonempirical test on the weight of pseudorandom number generators. In: Fang, K.T., et al. (eds.) Monte Carrlo and Quasi-Monte Carlo Methods 2000, pp. 381–395. Springer, Heidelberg (2002)

    Google Scholar 

  10. McCreight, E.M.: A space-economical suffix tree construction algorithm. J. ACM. 23, 262–272 (1976)

    Article  MATH  MathSciNet  Google Scholar 

  11. Schwartz, J.T., Sharir, M.: Identification of partially obscured objects in two and three dimensions by matching noisy characteristic curves. Intl. J. of Robotics Res. 6, 29–44 (1987)

    Article  Google Scholar 

  12. Shibuya, T.: Geometric Suffix Tree: A New Index Structure for Protein 3-D Structures. In: Lewenstein, M., Valiente, G. (eds.) CPM 2006. LNCS, vol. 4009, pp. 84–93. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  13. Ukkonen, E.: On-line construction of suffix-trees. Algorithmica 14, 249–260 (1995)

    Article  MATH  MathSciNet  Google Scholar 

  14. Weiner, P.: Linear pattern matching algorithms. In: Proc. 14th Symposium on Switching and Automata Theory, pp. 1–11 (1973)

    Google Scholar 

Download references

Author information

Authors and Affiliations


Editor information

Nivio Ziviani Ricardo Baeza-Yates

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Shibuya, T. (2007). Prefix-Shuffled Geometric Suffix Tree. In: Ziviani, N., Baeza-Yates, R. (eds) String Processing and Information Retrieval. SPIRE 2007. Lecture Notes in Computer Science, vol 4726. Springer, Berlin, Heidelberg.

Download citation

  • DOI:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-75529-6

  • Online ISBN: 978-3-540-75530-2

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics