{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T04:36:07Z","timestamp":1773808567916,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2019,12,12]],"date-time":"2019-12-12T00:00:00Z","timestamp":1576108800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001824","name":"Czech Science Foundation","doi-asserted-by":"publisher","award":["GA18-00258S"],"award-info":[{"award-number":["GA18-00258S"]}],"id":[{"id":"10.13039\/501100001824","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004585","name":"Brno University of Technology","doi-asserted-by":"publisher","award":["FIT-S-17-3964"],"award-info":[{"award-number":["FIT-S-17-3964"]}],"id":[{"id":"10.13039\/501100004585","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>https:\/\/pqsfinder.fi.muni.cz, https:\/\/bioconductor.org\/packages\/pqsfinder.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz928","type":"journal-article","created":{"date-parts":[[2019,12,9]],"date-time":"2019-12-09T20:11:29Z","timestamp":1575922289000},"page":"2584-2586","source":"Crossref","is-referenced-by-count":24,"title":["pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm"],"prefix":"10.1093","volume":"36","author":[{"given":"Dominika","family":"Labudov\u00e1","sequence":"first","affiliation":[{"name":"IT4Innovations Centre of Excellence, Faculty of Information Technology , Brno University of Technology, Brno 61266, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ji\u0159\u00ed","family":"Hon","sequence":"additional","affiliation":[{"name":"IT4Innovations Centre of Excellence, Faculty of Information Technology , Brno University of Technology, Brno 61266, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4213-5259","authenticated-orcid":false,"given":"Matej","family":"Lexa","sequence":"additional","affiliation":[{"name":"Department of Machine Learning and Data Processing, Faculty of Informatics, Masaryk University , Brno 60200, Czech Republic"},{"name":"Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences , Brno 61200, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,12,12]]},"reference":[{"key":"2023013110260382700_btz928-B1","doi-asserted-by":"crossref","first-page":"1746","DOI":"10.1093\/nar\/gkw006","article-title":"Re-evaluation of G-quadruplex propensity with G4Hunter","volume":"44","author":"Bedrat","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023013110260382700_btz928-B2","doi-asserted-by":"crossref","first-page":"lqz005","DOI":"10.1093\/nargab\/lqz005","article-title":"G4-iM Grinder: when size and frequency matter. g-quadruplex, i-motif and higher order structure search and analysis tool","volume":"2","author":"Belmonte-Reche","year":"2020","journal-title":"NAR Genomics Bioinform"},{"key":"2023013110260382700_btz928-B3","article-title":"QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable","volume":"35","author":"Berselli","year":"2019","journal-title":"Bioinformatics"},{"key":"2023013110260382700_btz928-B4","article-title":"High-throughput sequencing of DNA G-quadruplex structures in the human genome","volume":"33, 877\u2013881","author":"Chambers","year":"2015","journal-title":"Nat. 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