Publication Details
pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm
web application, G-quadruplex identification, G4, imperfect G4, potential
quadruplex-forming sequence, PQS, pattern search
Motivation: G-quadruplex is a DNA form in which four guanine-rich regions are
held together by Hoogsteen bonding 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 in vitro detection in isolated
DNA. In silico methods can be used to analyze nucleotide sequences for potential
quadruplex-forming sequences (PQS). We previously devised the pqsfinder algorithm
for identification of PQS, implemented it in C++ and published it 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
@article{BUT162286,
author="Dominika {Labudová} and Jiří {Hon} and Matej {Lexa}",
title="pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm",
journal="BIOINFORMATICS",
year="2020",
volume="36",
number="8",
pages="2584--2586",
doi="10.1093/bioinformatics/btz928",
issn="1367-4803",
url="https://www.fit.vut.cz/research/publication/12079/"
}