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

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 6.937

RIV identification code

RIV/00216224:14330/20:00114129

Organization unit

Faculty of Informatics

DOI

http://dx.doi.org/10.1093/bioinformatics/btz928

UT WoS

000537473400037

Keywords in English

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

Abstract

V originále

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

Citovat

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

@article{1652736,
   author = {Labudová, Dominika and Hon, Jiří and Lexa, Matej},
   article_location = {Oxford},
   article_number = {8},
   doi = {http://dx.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://dx.doi.org/10.1093/bioinformatics/btz928.

Detailed Information on Publication Record