pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F17%3A00094818" target="_blank" >RIV/00216224:14330/17:00094818 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216305:26230/17:PU126815

Výsledek na webu

<a href="https://academic.oup.com/bioinformatics/article-abstract/doi/10.1093/bioinformatics/btx413/3923794/pqsfinder-an-exhaustive-and-imperfection-tolerant" target="_blank" >https://academic.oup.com/bioinformatics/article-abstract/doi/10.1093/bioinformatics/btx413/3923794/pqsfinder-an-exhaustive-and-imperfection-tolerant</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/bioinformatics/btx413" target="_blank" >10.1093/bioinformatics/btx413</a>

Jazyk výsledku

angličtina

Název v původním jazyce

pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R

Popis výsledku v původním jazyce

Motivation: G-quadruplexes (G4s) are one of the non-B DNA structures easily observed in vitro and assumed to form in vivo. The latest experiments with G4-specific antibodies and G4-unwinding helicase mutants confirm this conjecture. These four-stranded structures have also been shown to influence a range of molecular processes in cells. As G4s are intensively studied, it is often desirable to screen DNA sequences and pinpoint the precise locations where they might form. Results: We describe and have tested a newly-developed Bioconductor package for identifying potential quadruplex-forming sequences (PQS). The package is easy-to-use, flexible and customizable. It allows for sequence searches that accommodate possible divergences from the optimal G4 base composition. A novel aspect of our research was the creation and training (parametrization) of an advanced scoring model which resulted in increased precision compared to similar tools. We demonstrate that the algorithm behind the searches has a 96% accuracy on 392 currently known and experimentally observed G4 structures. We also carried out searches against the recent G4-seq data to verify how well we can identify the structures detected by that technology. The correlation with pqsfinder predictionswas 0.622, higher than the correlation 0.491 obtained with the second best G4Hunter. Availability:http://bioconductor.org/packages/pqsfinder/ This paper is based on pqsfinder-1.4.1.

Název v anglickém jazyce

pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R

Popis výsledku anglicky

Motivation: G-quadruplexes (G4s) are one of the non-B DNA structures easily observed in vitro and assumed to form in vivo. The latest experiments with G4-specific antibodies and G4-unwinding helicase mutants confirm this conjecture. These four-stranded structures have also been shown to influence a range of molecular processes in cells. As G4s are intensively studied, it is often desirable to screen DNA sequences and pinpoint the precise locations where they might form. Results: We describe and have tested a newly-developed Bioconductor package for identifying potential quadruplex-forming sequences (PQS). The package is easy-to-use, flexible and customizable. It allows for sequence searches that accommodate possible divergences from the optimal G4 base composition. A novel aspect of our research was the creation and training (parametrization) of an advanced scoring model which resulted in increased precision compared to similar tools. We demonstrate that the algorithm behind the searches has a 96% accuracy on 392 currently known and experimentally observed G4 structures. We also carried out searches against the recent G4-seq data to verify how well we can identify the structures detected by that technology. The correlation with pqsfinder predictionswas 0.622, higher than the correlation 0.491 obtained with the second best G4Hunter. Availability:http://bioconductor.org/packages/pqsfinder/ This paper is based on pqsfinder-1.4.1.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

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

Rok uplatnění

2017

Kód důvěrnosti údajů

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

Název periodika

Bioinformatics

ISSN

1367-4803

e-ISSN

—

Svazek periodika

33

Číslo periodika v rámci svazku

21

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

7

Strana od-do

3373-3379

Kód UT WoS článku

000413645800006

EID výsledku v databázi Scopus

2-s2.0-85043369900