HON, Jiří, Tomáš MARTÍNEK, Jaroslav ZENDULKA and Matej LEXA. pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R. Bioinformatics, Oxford: Oxford University Press, 2017, vol. 33, No 21, p. 3373-3379. ISSN 1367-4803. doi:10.1093/bioinformatics/btx413.
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Basic information
Original name pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R
Authors HON, Jiří (203 Czechia), Tomáš MARTÍNEK (203 Czechia), Jaroslav ZENDULKA (203 Czechia) and Matej LEXA (703 Slovakia, guarantor, belonging to the institution).
Edition Bioinformatics, Oxford, Oxford University Press, 2017, 1367-4803.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10201 Computer sciences, information science, bioinformatics
Country of publisher United Kingdom of Great Britain and Northern Ireland
Confidentiality degree is not subject to a state or trade secret
WWW Hon et al. (2017)
Impact factor Impact factor: 5.481
RIV identification code RIV/00216224:14330/17:00094818
Organization unit Faculty of Informatics
Doi http://dx.doi.org/10.1093/bioinformatics/btx413
UT WoS 000413645800006
Keywords in English G4; G-quadruplex; R/Bioconductor; motif search; pattern search; DNA secondary structure
Tags International impact, Reviewed
Changed by Changed by: Ing. Matej Lexa, Ph.D., učo 31298. Changed: 13/3/2018 13:59.
Abstract
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.
Links
GA15-02891S, research and development projectName: Rostlinné transpozony a konformace DNA
Investor: Czech Science Foundation, Standard Projects
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