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. doi:10.1093/bioinformatics/btx413.
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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
Originální jazyk angličtina
Typ výsledku Článek v odborném periodiku
Obor 10201 Computer sciences, information science, bioinformatics
Stát vydavatele Velká Británie
Utajení není předmětem státního či obchodního tajemství
WWW 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
Změnil Změnil: Ing. Matej Lexa, Ph.D., učo 31298. Změněno: 13. 3. 2018 13:59.
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.
GA15-02891S, projekt VaVNázev: Rostlinné transpozony a konformace DNA
Investor: Grantová agentura ČR, Standardní projekty
VytisknoutZobrazeno: 15. 6. 2021 16:04