Towards faster matching algorithm using ternary tree in the area of genome mapping
The result's identifiers
Result code in 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>
Result on the web
<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>
Alternative languages
Result language
angličtina
Original language name
Towards faster matching algorithm using ternary tree in the area of genome mapping
Original language description
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.
Czech name
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Czech description
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Classification
Type
D - Article in proceedings
CEP classification
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OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Result continuities
Project
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Continuities
S - Specificky vyzkum na vysokych skolach
Others
Publication year
2020
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Article name in the collection
Advances in Intelligent Systems and Computing. Volume 1263
ISBN
978-3-030-57795-7
ISSN
2194-5357
e-ISSN
2194-5365
Number of pages
12
Pages from-to
413-424
Publisher name
Springer
Place of publication
Cham
Event location
Victoria
Event date
Aug 31, 2020
Type of event by nationality
WRD - Celosvětová akce
UT code for WoS article
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