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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