Algorithm of detecting structural variations in DNA sequences

Katarzyna Nałęcz-Charkiewicz; Robert Nowak

doi:10.1117/12.2074123

25 November 2014 Algorithm of detecting structural variations in DNA sequences

Katarzyna Nałęcz-Charkiewicz, Robert Nowak

Proceedings Volume 9290, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2014; 92901H (2014) https://doi.org/10.1117/12.2074123
Event: Symposium on Photonics Applications in Astronomy, Communications, Industry and High-Energy Physics Experiments, 2014, Warsaw, Poland

Abstract

Whole genome sequencing enables to use the longest common subsequence algorithm to detect genetic structure variations. We propose to search position of short unique fragments, genetic markers, to achieve acceptable time and space complexity. The markers are generated by algorithms searching the genetic sequence or its Fourier transformation. The presented methods are checked on structural variations generated in silico on bacterial genomes giving the comparable or better results than other solutions.

Citation Download Citation

Katarzyna Nałęcz-Charkiewicz and Robert Nowak "Algorithm of detecting structural variations in DNA sequences", Proc. SPIE 9290, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2014, 92901H (25 November 2014); https://doi.org/10.1117/12.2074123

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