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Genomecmp: computer software to detect genomic rearrangements using markers
Author(s): Maciej Kulawik; Robert M. Nowak
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Paper 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.

Paper Details

Date Published: 7 August 2017
PDF: 10 pages
Proc. SPIE 10445, Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017, 1044531 (7 August 2017); doi: 10.1117/12.2280483
Show Author Affiliations
Maciej Kulawik, Warsaw Univ. of Technology (Poland)
Robert M. Nowak, Warsaw Univ. of Technology (Poland)


Published in SPIE Proceedings Vol. 10445:
Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017
Ryszard S. Romaniuk; Maciej Linczuk, Editor(s)

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