Overlap detection for a genome assembly based on genomic signal processing

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26220%2F17%3APU125424" target="_blank" >RIV/00216305:26220/17:PU125424 - isvavai.cz</a>

Výsledek na webu

<a href="http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=8100282" target="_blank" >http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=8100282</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1109/CBMS.2017.140" target="_blank" >10.1109/CBMS.2017.140</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Overlap detection for a genome assembly based on genomic signal processing

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

Overlap detection for a genome assembly based on genomic signal processing

Popis výsledku anglicky

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.

Druh

D - Stať ve sborníku

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

<a href="/cs/project/GA17-01821S" target="_blank" >GA17-01821S: Výkonnostní techniky pro sestavování a anotaci bakteriálního genomu využívající číslicové zpracování genomických signálů</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2017

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název statě ve sborníku

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

ISBN

978-1-5386-1710-6

ISSN

2372-9198

e-ISSN

—

Počet stran výsledku

6

Strana od-do

301-305

Název nakladatele

IEEE Computer Society

Místo vydání

USA

Místo konání akce

Thessaloniki

Datum konání akce

22. 6. 2017

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

000424864800062