Publication detail

Overlap detection for a genome assembly based on genomic signal processing

JUGAS, R. SEDLÁŘ, K. ŠKUTKOVÁ, H. VÍTEK, M.

Original Title

Overlap detection for a genome assembly based on genomic signal processing

Type

conference paper

Language

English

Original Abstract

Although the genome sequences of most studied organisms, like human, E. coli, and others are already known, de novo genome sequencing remains popular as a majority of genomes remains unknown. Unfortunately, sequencing machines are able to read only short fragments of DNA. Therefore, one of the basic steps in reconstructing novel genomes lies in putting these pieces of DNA, called ‘reads’, together into complete genome sequences using a process known as genome assembly. Reads joining, however, requires efficient detection of their overlaps. This is commonly performed by comparing the particular characters (A, C, G, T) of the reads using string processing techniques. In this paper, we present an alternative way of detecting overlaps using genomic signal processing. Unlike string comparison, numerical phase signals reflect the complementarity of double stranded DNA making the signal ideal for effective strand independent overlap detection using covariance with high accuracy.

Keywords

assembly; overlap; genomic signal processing; covariance

Authors

JUGAS, R.; SEDLÁŘ, K.; ŠKUTKOVÁ, H.; VÍTEK, M.

Released

24. 7. 2017

Publisher

IEEE Computer Society

Location

USA

ISBN

978-1-5386-1710-6

Book

2017 IEEE 30th International Symposium on Computer-Based Medical Systems

ISBN

2372-9198

Periodical

Proceedings of the ... IEEE International Symposium on Computer-Based Medical Systems

Number

30

State

United States of America

Pages from

301

Pages to

305

Pages count

6

URL

http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=8100282

BibTex

@inproceedings{BUT141452,
  author="Robin {Jugas} and Karel {Sedlář} and Helena {Vítková} and Martin {Vítek}",
  title="Overlap detection for a genome assembly based on genomic signal processing",
  booktitle="2017 IEEE 30th International Symposium
on Computer-Based Medical Systems",
  year="2017",
  journal="Proceedings of the ... IEEE International Symposium on Computer-Based Medical Systems",
  number="30",
  pages="301--305",
  publisher="IEEE Computer Society",
  address="USA",
  doi="10.1109/CBMS.2017.140",
  isbn="978-1-5386-1710-6",
  issn="2372-9198",
  url="http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=8100282"
}