Backward Pattern Matching on Elastic Degenerate Strings

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68407700%3A21240%2F21%3A00349682" target="_blank" >RIV/68407700:21240/21:00349682 - isvavai.cz</a>

Výsledek na webu

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DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

Backward Pattern Matching on Elastic Degenerate Strings

Popis výsledku v původním jazyce

Recently, the concept of Elastic Degenerate Strings (EDS) was introduced as a way of representing a sequenced population of the same species. Several on-line Elastic Degenerate String Matching (EDSM) algorithms were presented so far. Some of them provide practical implementation. We propose a new on-line EDSM algorithm BNDM-EDS. Our algorithm combines two traditional algorithms BNDM and the Shift-And that were adapted to the specifics needed by Elastic Degenerate Strings. BNDM-EDS is running in O (Nmd m w e) worst-case time. This implies O (Nm) time for small patterns, where m is the length of the searched pattern, N is the size of EDS, and w is the size of the computer word. The algorithm uses O (N + n) space, where n is the length of EDS. BNDM-EDS requires a simple preprocessing step with time and space O (m). Experimental results on real genomic data show superiority of BNDM-EDS over state-of-the-art algorithms.

Název v anglickém jazyce

Backward Pattern Matching on Elastic Degenerate Strings

Popis výsledku anglicky

Recently, the concept of Elastic Degenerate Strings (EDS) was introduced as a way of representing a sequenced population of the same species. Several on-line Elastic Degenerate String Matching (EDSM) algorithms were presented so far. Some of them provide practical implementation. We propose a new on-line EDSM algorithm BNDM-EDS. Our algorithm combines two traditional algorithms BNDM and the Shift-And that were adapted to the specifics needed by Elastic Degenerate Strings. BNDM-EDS is running in O (Nmd m w e) worst-case time. This implies O (Nm) time for small patterns, where m is the length of the searched pattern, N is the size of EDS, and w is the size of the computer word. The algorithm uses O (N + n) space, where n is the length of EDS. BNDM-EDS requires a simple preprocessing step with time and space O (m). Experimental results on real genomic data show superiority of BNDM-EDS over state-of-the-art algorithms.

Druh

D - Stať ve sborníku

CEP obor

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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/GA19-20759S" target="_blank" >GA19-20759S: Efektivní vyhledávání řetězců pro Bioinformatiku</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

Proceedings of 14th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2021)

ISBN

978-989-758-490-9

ISSN

2184-4305

e-ISSN

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Počet stran výsledku

10

Strana od-do

50-59

Název nakladatele

SCITEPRESS – Science and Technology Publications, Lda

Místo vydání

Lisboa

Místo konání akce

Prague

Datum konání akce

11. 2. 2021

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

000664105700004