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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" }