Restriction Site Detection in Optical Mapping Data

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989100%3A27240%2F22%3A10252093" target="_blank" >RIV/61989100:27240/22:10252093 - isvavai.cz</a>

Výsledek na webu

<a href="https://link.springer.com/chapter/10.1007/978-3-031-14627-5_40" target="_blank" >https://link.springer.com/chapter/10.1007/978-3-031-14627-5_40</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1007/978-3-031-14627-5_40" target="_blank" >10.1007/978-3-031-14627-5_40</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Restriction Site Detection in Optical Mapping Data

Popis výsledku v původním jazyce

Optical Mapping is a method of DNA sequencing that is used to detect large structural variations in genomes. To create these optical maps a restriction enzyme is mixed with DNA. The enzyme binds to DNA and creates labels called restriction sites. These labels are captured by a camera where they appear as bright spots. This work introduces two methods to find these high-intensity points in optical maps. The first method is trying to find the peaks based only on intensity levels and the second is using a signal-to-noise ratio. Both methods have more than three parameters that can affect the results. Differential evolution and particle swarm optimization were used to find the best parameters that would give the highest accuracy. Bionano results were used as ground truth.

Název v anglickém jazyce

Restriction Site Detection in Optical Mapping Data

Popis výsledku anglicky

Optical Mapping is a method of DNA sequencing that is used to detect large structural variations in genomes. To create these optical maps a restriction enzyme is mixed with DNA. The enzyme binds to DNA and creates labels called restriction sites. These labels are captured by a camera where they appear as bright spots. This work introduces two methods to find these high-intensity points in optical maps. The first method is trying to find the peaks based only on intensity levels and the second is using a signal-to-noise ratio. Both methods have more than three parameters that can affect the results. Differential evolution and particle swarm optimization were used to find the best parameters that would give the highest accuracy. Bionano results were used as ground truth.

Druh

D - Stať ve sborníku

CEP obor

—

OECD FORD obor

10200 - Computer and information sciences

Projekt

—

Návaznosti

S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2022

Kód důvěrnosti údajů

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

Název statě ve sborníku

Lecture Notes in Networks and Systems. Volume 527

ISBN

978-3-031-14626-8

ISSN

2367-3370

e-ISSN

2367-3389

Počet stran výsledku

10

Strana od-do

393-402

Název nakladatele

Springer

Místo vydání

Cham

Místo konání akce

Sanda

Datum konání akce

7. 9. 2022

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

000870692600040