Skip to main content
SpringerLink
Log in

Toward Optimal Disk Layout of Genome Scale Suffix Trees

  • Conference paper
Simulated Evolution and Learning (SEAL 2010)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6457))

Included in the following conference series:

  • 2699 Accesses

Abstract

Suffix trees provide for efficient indexing of numerous sequence processing problems in biological databases. We address the pivotal issue of improving the search efficiency of disk-resident suffix trees by improving the storage layout from a statistical learning viewpoint. In particular, we make the following contributions: we (a) introduce the Q-Optimal Disk Layout(Q-OptDL) problem in the context of suffix trees and prove it to be NP-Hard, and (b) propose an algorithm for improving the layout of suffix trees that is guaranteed to perform asymptotically no worse than twice the optimal disk layout.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

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

    Book  MATH  Google Scholar 

  2. Bedathur, S.J., Haritsa, J.R.: Search- Optimized Suffix- Tree Storage for Biological Applications. In: Bader, D.A., Parashar, M., Sridhar, V., Prasanna, V.K. (eds.) HiPC 2005. LNCS, vol. 3769, pp. 29–39. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  3. Ko, P., Aluru, S.: Optimal self-adjusting trees for dynamic string data in secondary storage. In: Ziviani, N., Baeza-Yates, R. (eds.) SPIRE 2007. LNCS, vol. 4726, pp. 184–194. Springer, Heidelberg (2007)

    Chapter  Google Scholar 

  4. Kärkkäinen, J., Sanders, P., Burkhardt, S.: Linear work suffix array construction. JACM 53(6), 918–936 (2006)

    Article  MathSciNet  MATH  Google Scholar 

  5. Abouelhoda, M.I., Kurtz, S., Ohlebusch, E.: Replacing suffix trees with enhanced suffix arrays. J. Discrete Algorithms 2(1), 53–86 (2004)

    Article  MathSciNet  MATH  Google Scholar 

  6. Dementiev, R., Kärkkäinen, J., Mehnert, J., Sanders, P.: Better external memory suffix array construction. ACM Journal of Experimental Algorithmics 3.4, 12 (2008)

    MathSciNet  MATH  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. IBM Research, India

    Vikas K. Garg

Authors
  1. Vikas K. Garg
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Mechanical Engineering, Indian Institute of Technology Kanpur, 208016, Kanpur, Uttar Pradesh, India

    Kalyanmoy Deb

  2. Department of Computer Science andl Engineering, Indian Institute of Technology Kanpur, 208016, Kanpur, Uttar Pradesh, India

    Arnab Bhattacharya

  3. Department of Metallurgical and Materials Engineering, Indian Institute of Technology Kharagpur, 712302, Kharagpur, West Bengal, India

    Nirupam Chakraborti

  4. Department of Civil Engineering, Indian Institute of Technology Kanpur, 208016, Kanpur, Uttar Pradesh, India

    Partha Chakroborty  & Ashu Jain  & 

  5. Department of Electronics and Communication Engineering, Jadavpur University, 700032, Kolkata, West Bengal, India

    Swagatam Das

  6. Department of Mathematics and Statistics, Indian Institute of Technology Kanpur, 208016, Kanpur, Uttar Pradesh, India

    Joydeep Dutta

  7. Department of Chemical Engineering, Indian Institute of Technology Kanpur, 208016, Kanpur, Uttar Pradesh, India

    Santosh K. Gupta

  8. Aspiring Minds, 24 Pusa Road, 110005, New Delhi, India

    Varun Aggarwal

  9. Warwick Business School, University of Warwick, CV4 7AL, Coventry, UK

    Jürgen Branke

  10. Department of Computer Science and Engineering, University of Nevada, 89557, Reno, NV, USA

    Sushil J. Louis

  11. Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering Drive 3, 117576, Singapore

    Kay Chen Tan

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Garg, V.K. (2010). Toward Optimal Disk Layout of Genome Scale Suffix Trees. In: Deb, K., et al. Simulated Evolution and Learning. SEAL 2010. Lecture Notes in Computer Science, vol 6457. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-17298-4_80

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-17298-4_80

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-17297-7

  • Online ISBN: 978-3-642-17298-4

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation