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

Result code in 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>

Alternative codes found

RIV/00216305:26230/17:PU126815

Result on the web

<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>

Result language

angličtina

Original language name

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

Original language description

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.

Czech name

—

Czech description

—

Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

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

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

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

Publication year

2017

Confidentiality

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

Name of the periodical

Bioinformatics

ISSN

1367-4803

e-ISSN

—

Volume of the periodical

33

Issue of the periodical within the volume

21

Country of publishing house

GB - UNITED KINGDOM

Number of pages

7

Pages from-to

3373-3379

UT code for WoS article

000413645800006

EID of the result in the Scopus database

2-s2.0-85043369900