Towards faster matching algorithm using ternary tree in the area of genome mapping

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989100%3A27240%2F20%3A10246981" target="_blank" >RIV/61989100:27240/20:10246981 - isvavai.cz</a>

Výsledek na webu

<a href="https://link.springer.com/chapter/10.1007%2F978-3-030-57796-4_40" target="_blank" >https://link.springer.com/chapter/10.1007%2F978-3-030-57796-4_40</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1007/978-3-030-57796-4_40" target="_blank" >10.1007/978-3-030-57796-4_40</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Towards faster matching algorithm using ternary tree in the area of genome mapping

Popis výsledku v původním jazyce

In area of precision medicine there is a need to map long sequences of DNA, which are represented as strings of characters or numbers. Most of the computer programs used for genome mapping use suffix-based data structures, but those are much more suitable for mapping of short DNA sequences represented as strings over small alphabets. The most crucial parameters of data structure used for DNA mapping are time to fill the data structure, search time and system resources needed, especially memory, as the amount of data from scanning process can be really large. This article will describe implementation of memory optimized Ternary Search Tree (TST) for indexing of positions of labels obtained by Bionano Genomics DNA imaging device. BNX file parser with alphabet encoding functions is described and performance results from experiments with presented software solution on real data from Bionano Genomics Saphyr device are also included. (C) Springer Nature Switzerland AG 2021.

Název v anglickém jazyce

Towards faster matching algorithm using ternary tree in the area of genome mapping

Popis výsledku anglicky

In area of precision medicine there is a need to map long sequences of DNA, which are represented as strings of characters or numbers. Most of the computer programs used for genome mapping use suffix-based data structures, but those are much more suitable for mapping of short DNA sequences represented as strings over small alphabets. The most crucial parameters of data structure used for DNA mapping are time to fill the data structure, search time and system resources needed, especially memory, as the amount of data from scanning process can be really large. This article will describe implementation of memory optimized Ternary Search Tree (TST) for indexing of positions of labels obtained by Bionano Genomics DNA imaging device. BNX file parser with alphabet encoding functions is described and performance results from experiments with presented software solution on real data from Bionano Genomics Saphyr device are also included. (C) Springer Nature Switzerland AG 2021.

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

—

Návaznosti

S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2020

Kód důvěrnosti údajů

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

Název statě ve sborníku

Advances in Intelligent Systems and Computing. Volume 1263

ISBN

978-3-030-57795-7

ISSN

2194-5357

e-ISSN

2194-5365

Počet stran výsledku

12

Strana od-do

413-424

Název nakladatele

Springer

Místo vydání

Cham

Místo konání akce

Victoria

Datum konání akce

31. 8. 2020

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

—