Detail publikace

Overlap detection for a genome assembly based on genomic signal processing

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

Originální název

Overlap detection for a genome assembly based on genomic signal processing

Typ

článek ve sborníku ve WoS nebo Scopus

Jazyk

angličtina

Originální abstrakt

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.

Klíčová slova

assembly; overlap; genomic signal processing; covariance

Autoři

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

Vydáno

24. 7. 2017

Nakladatel

IEEE Computer Society

Místo

USA

ISBN

978-1-5386-1710-6

Kniha

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

ISSN

2372-9198

Periodikum

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

Číslo

30

Stát

Spojené státy americké

Strany od

301

Strany do

305

Strany počet

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"
}