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

J 2017

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

HON, Jiří, Tomáš MARTÍNEK, Jaroslav ZENDULKA a Matej LEXA

Základní údaje

Originální název

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

Autoři

HON, Jiří (203 Česká republika), Tomáš MARTÍNEK (203 Česká republika), Jaroslav ZENDULKA (203 Česká republika) a Matej LEXA (703 Slovensko, garant, domácí)

Vydání

Bioinformatics, Oxford, Oxford University Press, 2017, 1367-4803

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

Hon et al. (2017)

Impakt faktor

Impact factor: 5.481

Kód RIV

RIV/00216224:14330/17:00094818

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1093/bioinformatics/btx413

UT WoS

000413645800006

Klíčová slova anglicky

G4; G-quadruplex; R/Bioconductor; motif search; pattern search; DNA secondary structure

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 13. 3. 2018 13:59, doc. Ing. Matej Lexa, Ph.D.

Anotace

V originále

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.

Návaznosti

GA15-02891S, projekt VaV

Název: Rostlinné transpozony a konformace DNA

Investor: Grantová agentura ČR, Rostlinné transpozony a konformace DNA

Citovat

HON, Jiří, Tomáš MARTÍNEK, Jaroslav ZENDULKA a Matej LEXA. pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R. Bioinformatics. Oxford: Oxford University Press, 2017, roč. 33, č. 21, s. 3373-3379. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btx413.

@article{1384802,
   author = {Hon, Jiří and Martínek, Tomáš and Zendulka, Jaroslav and Lexa, Matej},
   article_location = {Oxford},
   article_number = {21},
   doi = {http://dx.doi.org/10.1093/bioinformatics/btx413},
   keywords = {G4; G-quadruplex; R/Bioconductor; motif search; pattern search; DNA secondary structure},
   language = {eng},
   issn = {1367-4803},
   journal = {Bioinformatics},
   title = {pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R},
   url = {https://academic.oup.com/bioinformatics/article-abstract/doi/10.1093/bioinformatics/btx413/3923794/pqsfinder-an-exhaustive-and-imperfection-tolerant},
   volume = {33},
   year = {2017}
}

TY  - JOUR
ID  - 1384802
AU  - Hon, Jiří - Martínek, Tomáš - Zendulka, Jaroslav - Lexa, Matej
PY  - 2017
TI  - pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R
JF  - Bioinformatics
VL  - 33
IS  - 21
SP  - 3373-3379
EP  - 3373-3379
PB  - Oxford University Press
SN  - 13674803
KW  - G4
KW  - G-quadruplex
KW  - R/Bioconductor
KW  - motif search
KW  - pattern search
KW  - DNA secondary structure
UR  - https://academic.oup.com/bioinformatics/article-abstract/doi/10.1093/bioinformatics/btx413/3923794/pqsfinder-an-exhaustive-and-imperfection-tolerant
L2  - https://academic.oup.com/bioinformatics/article-abstract/doi/10.1093/bioinformatics/btx413/3923794/pqsfinder-an-exhaustive-and-imperfection-tolerant
N2  - 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.
ER  -

HON, Jiří, Tomáš MARTÍNEK, Jaroslav ZENDULKA a Matej LEXA. pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R. \textit{Bioinformatics}. Oxford: Oxford University Press, 2017, roč.~33, č.~21, s.~3373-3379. ISSN~1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btx413.

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