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Efficient Transformation of Protein Sequence Databases to Columnar Index Schema

  • Roman ZounEmail author
  • Kay Schallert
  • David Broneske
  • Ivayla Trifonova
  • Xiao Chen
  • Robert Heyer
  • Dirk Benndorf
  • Gunter Saake
Conference paper
Part of the Communications in Computer and Information Science book series (CCIS, volume 1062)

Abstract

Mass spectrometry is used to sequence proteins and extract bio-markers of biological environments. These bio-markers can be used to diagnose thousands of diseases and optimize biological environments such as bio-gas plants. Indexing of the protein sequence data allows to streamline the experiments and speed up the analysis. In our work, we present a schema for distributed column-based database management systems using a column-oriented index to store sequence data. This leads to the problem, how to transform the protein sequence data from the standard format to the new schema. We analyze four different methods of transformation and evaluate those four different methods. The results show that our proposed extended radix tree has the best performance regarding memory consumption and calculation time. Hence, the radix tree is proved to be a suitable data structure for the transformation of protein sequences into the indexed schema.

Keywords

Trie Radix tree Storage system Sequence data 

Notes

Acknowledgments

The authors sincerely thank Niya Zoun, Gabriel Cam-pero Durand, Marcus Pinnecke, Sebastian Krieter, Sven Helmer, Sven Brehmer and Andreas Meister for their support and advice. This work is partly funded by the BMBF (Fkz: 031L0103), the European Regional Development Fund (no.: 11.000sz00.00.0 17 114347 0), the DFG (grant no.: SA 465/50-1), by the German Federal Ministry of Food and Agriculture (grants no.: 22404015) and dedicated to the memory of Mikhail Zoun.

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Roman Zoun
    • 1
    Email author
  • Kay Schallert
    • 1
  • David Broneske
    • 1
  • Ivayla Trifonova
    • 1
  • Xiao Chen
    • 1
  • Robert Heyer
    • 1
  • Dirk Benndorf
    • 2
  • Gunter Saake
    • 1
  1. 1.University of MagdeburgMagdeburgGermany
  2. 2.Max Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany

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