Genomecmp: computer software to detect genomic rearrangements using markers

Maciej Kulawik; Robert M. Nowak

doi:10.1117/12.2280483

7 August 2017 Genomecmp: computer software to detect genomic rearrangements using markers

Maciej Kulawik, Robert M. Nowak

Proceedings Volume 10445, Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017; 1044531 (2017) https://doi.org/10.1117/12.2280483
Event: Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2017, 2017, Wilga, Poland

Abstract

Detection of genomics rearrangements is a tough task, because of the size of data to be processed. As genome sequences may consist of hundreds of millions symbols, it is not only practically impossible to compare them by hand, but it is also complex problem for computer software. The way to significantly accelerate the process is to use rearrangement detection algorithm based on unique short sequences called markers. The algorithm described in this paper develops markers using base genome and find the markers positions on other genome. The algorithm has been extended by support for ambiguity symbols.

Web application with graphical user interface has been created using three-layer architecture, where users could run the task simultaneously.

The accuracy and efficiency of proposed solution has been studied using generated and real data.

Citation Download Citation

Maciej Kulawik and Robert M. Nowak "Genomecmp: computer software to detect genomic rearrangements using markers", Proc. SPIE 10445, Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017, 1044531 (7 August 2017); https://doi.org/10.1117/12.2280483

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