pqsfinder web: G-quadruplex prediction using optimized
pqsfinder algorithm

J 2020

pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm

LABUDOVÁ, Dominika; Jiří HON and Matej LEXA

Basic information

Original name

pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm

Authors

LABUDOVÁ, Dominika (703 Slovakia); Jiří HON (203 Czech Republic, guarantor) and Matej LEXA (703 Slovakia, belonging to the institution)

Edition

Bioinformatics, Oxford, Oxford University Press, 2020, 1367-4803

Other information

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

References:

URL

Impact factor

Impact factor: 6.937

RIV identification code

RIV/00216224:14330/20:00114129

Organization unit

Faculty of Informatics

DOI

https://doi.org/10.1093/bioinformatics/btz928

UT WoS

000537473400037

EID Scopus

2-s2.0-85084028047

Keywords in English

g4; g-quadruplex; software; R/Bioconductor; sequence analysis

Abstract

In the original language

Motivation: G-quadruplex is a DNA or RNA form in which four guanine-rich regions are held together by base pairing between guanine nucleotides in coordination with potassium ions. G-quadruplexes are increasingly seen as a biologically important component of genomes. Their detection in vivo is problematic; however, sequencing and spectrometric techniques exist for their in vitro detection. We previously devised the pqsfinder algorithm for PQS identification, implemented it in C++ and published as an R/Bioconductor package. We looked for ways to optimize pqsfinder for faster and user-friendly sequence analysis. Results: We identified two weak points where pqsfinder could be optimized. We modified the internals of the recursive algorithm to avoid matching and scoring many sub-optimal PQS conformations that are later discarded. To accommodate the needs of a broader range of users, we created a website for submission of sequence analysis jobs that does not require knowledge of R to use pqsfinder.

Links

GA18-00258S, research and development project

Name: Úloha transposonů v dynamice rostlinných genomů (Acronym: TRANSPOSONY_DRG)

Investor: Czech Science Foundation

Cite

LABUDOVÁ, Dominika; Jiří HON and Matej LEXA. pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm. Bioinformatics. Oxford: Oxford University Press, 2020, vol. 36, No 8, p. 2584-2586. ISSN 1367-4803. Available from: https://doi.org/10.1093/bioinformatics/btz928.

@article{1652736,
   author = {Labudová, Dominika and Hon, Jiří and Lexa, Matej},
   article_location = {Oxford},
   article_number = {8},
   doi = {https://doi.org/10.1093/bioinformatics/btz928},
   keywords = {g4; g-quadruplex; software; R/Bioconductor; sequence analysis},
   language = {eng},
   issn = {1367-4803},
   journal = {Bioinformatics},
   title = {pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm},
   url = {https://academic.oup.com/bioinformatics/article/36/8/2584/5674042},
   volume = {36},
   year = {2020}
}

TY  - JOUR
ID  - 1652736
AU  - Labudová, Dominika - Hon, Jiří - Lexa, Matej
PY  - 2020
TI  - pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm
JF  - Bioinformatics
VL  - 36
IS  - 8
SP  - 2584-2586
EP  - 2584-2586
PB  - Oxford University Press
SN  - 13674803
KW  - g4
KW  - g-quadruplex
KW  - software
KW  - R/Bioconductor
KW  - sequence analysis
UR  - https://academic.oup.com/bioinformatics/article/36/8/2584/5674042
N2  - Motivation: G-quadruplex is a DNA or RNA form in which four guanine-rich regions are held together by base pairing between guanine nucleotides in coordination with potassium ions. G-quadruplexes are increasingly seen as a biologically important component of genomes. Their detection in vivo is problematic; however, sequencing and spectrometric techniques exist for their in vitro detection. We previously devised the pqsfinder algorithm for PQS identification, implemented it in C++ and published as an R/Bioconductor package. We looked for ways to optimize pqsfinder for faster and user-friendly sequence analysis. Results: We identified two weak points where pqsfinder could be optimized. We modified the internals of the recursive algorithm to avoid matching and scoring many sub-optimal PQS conformations that are later discarded. To accommodate the needs of a broader range of users, we created a website for submission of sequence analysis jobs that does not require knowledge of R to use pqsfinder.
ER  -

LABUDOVÁ, Dominika; Jiří HON and Matej LEXA. pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm. \textit{Bioinformatics}. Oxford: Oxford University Press, 2020, vol.~36, No~8, p.~2584-2586. ISSN~1367-4803. Available from: https://doi.org/10.1093/bioinformatics/btz928.

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