DISTRIBUTED FREQUENCY SORTING IN SPECTRAL VIDEO ANALYSIS OF DNA SEQUENCES

Anca Bucur, Jasper van Leeuwen, Nevenka Dimitrova

Abstract

DNA spectral analysis, i.e. the analysis of DNA spectrograms, has been proposed as a method to systematically investigate DNA patterns, which may correspond to relevant biological features. The Frequency Sorting method sorts the sequences in spectral domain based on their frequency content, and detects and groups those sequences exhibiting one or more strong patterns in the same frequencies. In this paper we propose a novel distributed algorithm for Frequency Sorting and report on the performance results of our implementation for the alignment in spectral domain of the human chromosome 21. Distributed Frequency Sorting enables efficient spectral alignment and allows for the easy detection of strong patterns in both single and multiple frequencies.

References

  1. D. Anastassiou, 2000. Frequency-domain analysis of biomolecular sequences. In Bioinformatics 16(12), p. 1073-1081, 2000.
  2. A. Bucur et al., 2008. A Frequency Sorting Method for Spectral Analysis of DNA Sequences. In BIBM, 2008.
  3. E. Santo et al., 2007. Improvement of Spectral Analysis as a Genomic Analysis Tool. In IEEE Workshop on Genomic Signal Processing and Statistics, p. 1-4, 2007.
  4. D. Sussillo et al., 2004. Spectrogram Analysis of Genomes. In EURASIP Journal on Applied Signal Processing, Special Issue on Processing 2004 (1), p. 29-42, 2004.
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Paper Citation


in Harvard Style

Bucur A., van Leeuwen J. and Dimitrova N. (2010). DISTRIBUTED FREQUENCY SORTING IN SPECTRAL VIDEO ANALYSIS OF DNA SEQUENCES . In Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010) ISBN 978-989-674-019-1, pages 207-210. DOI: 10.5220/0002713302070210


in Bibtex Style

@conference{bioinformatics10,
author={Anca Bucur and Jasper van Leeuwen and Nevenka Dimitrova},
title={DISTRIBUTED FREQUENCY SORTING IN SPECTRAL VIDEO ANALYSIS OF DNA SEQUENCES},
booktitle={Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)},
year={2010},
pages={207-210},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002713302070210},
isbn={978-989-674-019-1},
}


in EndNote Style

TY - CONF
JO - Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)
TI - DISTRIBUTED FREQUENCY SORTING IN SPECTRAL VIDEO ANALYSIS OF DNA SEQUENCES
SN - 978-989-674-019-1
AU - Bucur A.
AU - van Leeuwen J.
AU - Dimitrova N.
PY - 2010
SP - 207
EP - 210
DO - 10.5220/0002713302070210