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Non-repetitive DNA Sequence Compression Using Memoization

  • K. G. Srinivasa
  • M. Jagadish
  • K. R. Venugopal
  • L. M. Patnaik
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4345)

Abstract

With increasing number of DNA sequences being discovered the problem of storing and using genomic databases has become vital. Since DNA sequences consist of only four letters, two bits are sufficient to store each base. Many algorithms have been proposed in the recent past that push the bits/base limit further. The subtle patterns in DNA along with statistical inferences have been exploited to increase the compression ratio. From the compression perspective, the entire DNA sequences can be considered to be made of two types of sequences: repetitive and non-repetitive. The repetitive parts are compressed used dictionary-based schemes and non-repetitive sequences of DNA are usually compressed using general text compression schemes. In this paper, we present a memoization based encoding scheme for non-repeat DNA sequences. This scheme is incorporated with a DNA-specific compression algorithm, DNAPack, which is used for compression of DNA sequences. The results show that our method noticeably performs better than other techniques of its kind.

Keywords

DNA Compression Memoization Text Compression 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • K. G. Srinivasa
    • 1
  • M. Jagadish
    • 2
  • K. R. Venugopal
    • 3
  • L. M. Patnaik
    • 4
  1. 1.Data Mining LaboratoryM S Ramaiah Institute of TechnologyBangalore
  2. 2.Software Engineer, MindTree ConsultingBangalore
  3. 3.Professor, University of Visvesvaraya College of EngineeringBangalore UniversityBangalore
  4. 4.Professor, Microprocessor Application LaboratoryIndian Institute of ScienceBangalore

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