Publication result detail

Application of Optimization Algorithms to the Genome Assembly

JUGAS, R.

Original Title

Application of Optimization Algorithms to the Genome Assembly

English Title

Application of Optimization Algorithms to the Genome Assembly

Type

Paper in proceedings (conference paper)

Original 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 simi-larity 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 graph-theory-based algorithms.

English 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 simi-larity 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 graph-theory-based algorithms.

Keywords

bioinformatics, genome assembly, genomic signal processing, optimization techniques

Key words in English

bioinformatics, genome assembly, genomic signal processing, optimization techniques

Authors

JUGAS, R.

RIV year

2019

Released

26.04.2018

Publisher

Vysoké učení technické v Brně, Fakulta elektrotechniky a komunikačních

Location

Brno

ISBN

978-80-214-5614-3

Book

Proceedings of the 24th Conference STUDENT EEICT 2018

Pages from

595

Pages to

599

Pages count

5

BibTex

@inproceedings{BUT147132,
  author="Robin {Jugas}",
  title="Application of Optimization Algorithms to the Genome Assembly",
  booktitle="Proceedings of the 24th Conference STUDENT EEICT 2018",
  year="2018",
  number="1",
  pages="595--599",
  publisher="Vysoké učení technické v Brně, Fakulta elektrotechniky a komunikačních",
  address="Brno",
  isbn="978-80-214-5614-3"
}