Publication details

pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm

Authors

LABUDOVÁ Dominika HON Jiří LEXA Matej

Year of publication 2020
Type Article in Periodical
Magazine / Source Bioinformatics
MU Faculty or unit

Faculty of Informatics

Citation
Web https://academic.oup.com/bioinformatics/article/36/8/2584/5674042
Doi http://dx.doi.org/10.1093/bioinformatics/btz928
Keywords g4; g-quadruplex; software; R/Bioconductor; sequence analysis
Description 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.
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