Analysis of Optical Mapping Data with Neural Network

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989100%3A27240%2F21%3A10248618" target="_blank" >RIV/61989100:27240/21:10248618 - isvavai.cz</a>

Výsledek na webu

<a href="https://link.springer.com/chapter/10.1007/978-3-030-84910-8_26" target="_blank" >https://link.springer.com/chapter/10.1007/978-3-030-84910-8_26</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1007/978-3-030-84910-8_26" target="_blank" >10.1007/978-3-030-84910-8_26</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Analysis of Optical Mapping Data with Neural Network

Popis výsledku v původním jazyce

Optical Mapping is a method of DNA sequencing, that can be used to detect large structural variations in genomes. To create these optical maps, a restriction enzyme is mixed with DNA where the enzyme binds to DNA creating labels called restriction sites. These restriction sites and can be captured by fluorescent microscope with a camera. One of the tools that can capture these images is Bionano Genomics Saphyr mapping instrument. Their system produces high-resolution images of DNA molecules with restriction sites and their software detects them. Molecules in these images are visualized by gray lines with restrictions sites appearing brighter. Some of these molecules have very low brightness and with static noise around them, they are almost indistinguishable from the background. This work proposes GPU accelerated method for molecule detection. A neural network was used for molecule segmentation from the image and the dataset for the network was created from the results of Bionano Genomics tools. This detection method can be used as a substitute for restriction map detection in the Bionano Genomics processing pipeline or as a tool that can highlight the regions of interest in the raw optical maps images. (C) 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

Název v anglickém jazyce

Analysis of Optical Mapping Data with Neural Network

Popis výsledku anglicky

Optical Mapping is a method of DNA sequencing, that can be used to detect large structural variations in genomes. To create these optical maps, a restriction enzyme is mixed with DNA where the enzyme binds to DNA creating labels called restriction sites. These restriction sites and can be captured by fluorescent microscope with a camera. One of the tools that can capture these images is Bionano Genomics Saphyr mapping instrument. Their system produces high-resolution images of DNA molecules with restriction sites and their software detects them. Molecules in these images are visualized by gray lines with restrictions sites appearing brighter. Some of these molecules have very low brightness and with static noise around them, they are almost indistinguishable from the background. This work proposes GPU accelerated method for molecule detection. A neural network was used for molecule segmentation from the image and the dataset for the network was created from the results of Bionano Genomics tools. This detection method can be used as a substitute for restriction map detection in the Bionano Genomics processing pipeline or as a tool that can highlight the regions of interest in the raw optical maps images. (C) 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

Druh

D - Stať ve sborníku

CEP obor

—

OECD FORD obor

10200 - Computer and information sciences

Projekt

<a href="/cs/project/NU20-06-00269" target="_blank" >NU20-06-00269: Využití buněčných profilů a proteomiky synoviální tekutiny, případně tkání pro podporu klinického rozhodování u osteoartrózy kolena</a><br>

Návaznosti

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

Rok uplatnění

2021

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 312

ISBN

978-3-030-84909-2

ISSN

2367-3370

e-ISSN

2367-3389

Počet stran výsledku

10

Strana od-do

243-252

Název nakladatele

Springer

Místo vydání

Cham

Místo konání akce

Tchaj-čung

Datum konání akce

1. 9. 2021

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

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