On-line Searching in IUPAC nucleotide sequences

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68407700%3A21240%2F19%3A00338889" target="_blank" >RIV/68407700:21240/19:00338889 - isvavai.cz</a>

Výsledek na webu

<a href="http://www.biostec.org/?y=2019" target="_blank" >http://www.biostec.org/?y=2019</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.5220/0007382900660077" target="_blank" >10.5220/0007382900660077</a>

Jazyk výsledku

angličtina

Název v původním jazyce

On-line Searching in IUPAC nucleotide sequences

Popis výsledku v původním jazyce

We propose a novel pattern matching algorithm for consensus nucleotide sequences over IUPAC alphabet, called BADPM (Byte-Aligned Degenerate Pattern Matching). The consensus nucleotide sequences represent a consensus obtained by sequencing a population of the same species and they are considered as so-called degenerate strings. BADPM works at the level of single bytes and it achieves sublinear search time on average. The algorithm is based on tabulating all possible factors of the searched pattern. It needs O (m + mα2 log m)-space data structure and O(mα2 ) time for preprocessing where m is a length of the pattern and α represents a maximum number of variants implied from a 4-gram over IUPAC alphabet. The worst-case locate time is bounded by O (nm2α4 ) for BADPM where n is the length of the input text. However, the experiments performed on real genomic data proved the sublinear search time. BADPM can easily cooperate with the block q-gram inverted index and so achieve still better locate time. We implemented two other pattern matching algorithms for IUPAC nucleotide sequences as a baseline: Boyer-Moore-Horspool (BMH) and Parallel Naive Search (PNS). Especially PNS proves its efficiency insensitive to the length of the searched pattern m. BADPM proved its strong superiority for searching middle and long patterns.

Název v anglickém jazyce

On-line Searching in IUPAC nucleotide sequences

Popis výsledku anglicky

We propose a novel pattern matching algorithm for consensus nucleotide sequences over IUPAC alphabet, called BADPM (Byte-Aligned Degenerate Pattern Matching). The consensus nucleotide sequences represent a consensus obtained by sequencing a population of the same species and they are considered as so-called degenerate strings. BADPM works at the level of single bytes and it achieves sublinear search time on average. The algorithm is based on tabulating all possible factors of the searched pattern. It needs O (m + mα2 log m)-space data structure and O(mα2 ) time for preprocessing where m is a length of the pattern and α represents a maximum number of variants implied from a 4-gram over IUPAC alphabet. The worst-case locate time is bounded by O (nm2α4 ) for BADPM where n is the length of the input text. However, the experiments performed on real genomic data proved the sublinear search time. BADPM can easily cooperate with the block q-gram inverted index and so achieve still better locate time. We implemented two other pattern matching algorithms for IUPAC nucleotide sequences as a baseline: Boyer-Moore-Horspool (BMH) and Parallel Naive Search (PNS). Especially PNS proves its efficiency insensitive to the length of the searched pattern m. BADPM proved its strong superiority for searching middle and long patterns.

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

<a href="/cs/project/EF16_019%2F0000765" target="_blank" >EF16_019/0000765: Výzkumné centrum informatiky</a><br>

Návaznosti

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

Rok uplatnění

2019

Kód důvěrnosti údajů

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

Název statě ve sborníku

Proceedings of 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019)

ISBN

978-989-758-353-7

ISSN

2184-4305

e-ISSN

—

Počet stran výsledku

12

Strana od-do

66-77

Název nakladatele

SCITEPRESS – Science and Technology Publications, Lda

Místo vydání

Lisboa

Místo konání akce

Praha

Datum konání akce

22. 2. 2019

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

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