Original title: Application Of Optimization Algorithms To The Genome Assembly
Authors: Jugas, Robin
Document type: Papers
Language: eng
Publisher: Vysoké učení technické v Brně, Fakulta elektrotechniky a komunikačních technologií
Abstract: The paper results from development of new sequencing methods together with the need of suitable genome assembly algorithms. It combines the genomic signal processing, correlation techniques and optimization algorithms for solving assembly task. Genomic signals are made by conversion of letter-based DNA into the form of digital signal, thus the methods of digital signal processing can be applied. Possible overlaps between reads converted into signals are found by computing correlation coefficient similarly to cross-correlation. We acquire similarity matrix and the task is to find the path through it achieving minimum distance criterion. For the task, the two optimization techniques were employed: ant colony optimization (ACO) and simulated annealing (SA). The result implies the possibility of using the ACO at the task of creating path through similarly to graphtheory-based algorithms.
Keywords: bioinformatics; genome assembly; genomic signal processing; optimization tec
Host item entry: Proceedings of the 24th Conference STUDENT EEICT 2018, ISBN 978-80-214-5614-3

Institution: Brno University of Technology (web)
Document availability information: Fulltext is available in the Brno University of Technology Digital Library.
Original record: http://hdl.handle.net/11012/138303

Permalink: http://www.nusl.cz/ntk/nusl-393489


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