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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))

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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.

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References

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Author information

Authors and Affiliations

  1. IBM Research, India

    Vikas K. Garg

Authors
  1. Vikas K. Garg
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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

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© 2010 Springer-Verlag Berlin Heidelberg

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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

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  • 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)

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