| LABUDOVÁ, Dominika, Jiří HON a Matej LEXA. pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm. Bioinformatics. Oxford: Oxford University Press, 2020, roč. 36, č. 8, s. 2584-2586. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btz928. |
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@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 a Matej LEXA. pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm. \textit{Bioinformatics}. Oxford: Oxford University Press, 2020, roč.~36, č.~8, s.~2584-2586. ISSN~1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btz928.
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