Relative Lempel-Ziv Compression of Genomes for Large-Scale Storage and Retrieval

  • Shanika Kuruppu
  • Simon J. Puglisi
  • Justin Zobel
Conference paper

DOI: 10.1007/978-3-642-16321-0_20

Part of the Lecture Notes in Computer Science book series (LNCS, volume 6393)
Cite this paper as:
Kuruppu S., Puglisi S.J., Zobel J. (2010) Relative Lempel-Ziv Compression of Genomes for Large-Scale Storage and Retrieval. In: Chavez E., Lonardi S. (eds) String Processing and Information Retrieval. SPIRE 2010. Lecture Notes in Computer Science, vol 6393. Springer, Berlin, Heidelberg

Abstract

Self-indexes – data structures that simultaneously provide fast search of and access to compressed text – are promising for genomic data but in their usual form are not able to exploit the high level of replication present in a collection of related genomes. Our ‘RLZ’ approach is to store a self-index for a base sequence and then compress every other sequence as an LZ77 encoding relative to the base. For a collection of r sequences totaling N bases, with a total of s point mutations from a base sequence of length n, this representation requires just \(nH_k(T) + s\log n + s\log \frac{N}{s} + O(s)\) bits. At the cost of negligible extra space, access to ℓ consecutive symbols requires \(\O(\ell + \log n)\) time. Our experiments show that, for example, RLZ can represent individual human genomes in around 0.1 bits per base while supporting rapid access and using relatively little memory.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Shanika Kuruppu
    • 1
  • Simon J. Puglisi
    • 2
  • Justin Zobel
    • 1
  1. 1.National ICT Australia, Department of Computer Science & Software EngineeringUniversity of Melbourne 
  2. 2.School of Computer Science and Information TechnologyRoyal Melbourne Institute of TechnologyAustralia

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