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NET-ASAR: A Tool for DNA Sequence Search Based on Data Compression

  • Manuel Gaspar
  • Diogo Pratas
  • Armando J. Pinho
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 803)

Abstract

The great increase in the amount of sequenced DNA has created a problem: the storage of the sequences. As such, data compression techniques, designed specifically to compress genetic information, is an important area of research and development. Likewise, the ability to search similar DNA sequences in relation to a larger sequence, such as a chromosome, has a really important role in the study of organisms and the possible connection between different species. This paper proposes NET-ASAR, a tool for DNA sequence search, based on data compression, or, specifically, finite-context models, by obtaining a measure of similarity between a reference and a target. The method uses an approach based on finite-context models for the creation of a statistical model of the reference sequence and obtaining the estimated number of bits necessary for the encoding of the target sequence, using the reference model. NET-ASAR is freely available, under license GPLv3, at https://github.com/manuelgaspar/NET-ASAR.

Keywords

DNA sequence search Data compression Finite-context models Similarity 

Notes

Acknowledgments

This work was partially funded by National Funds through the FCT - Foundation for Science and Technology (UID/CEC/00127/2013, PTDC/EEI-SII/6608/2014).

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Manuel Gaspar
    • 1
  • Diogo Pratas
    • 1
  • Armando J. Pinho
    • 1
  1. 1.IEETAUniversity of AveiroAveiroPortugal

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