{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T12:35:41Z","timestamp":1763037341404,"version":"3.37.3"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2019,7,22]],"date-time":"2019-07-22T00:00:00Z","timestamp":1563753600000},"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\/501100003500","name":"University of Padova","doi-asserted-by":"publisher","award":["TOPP_SID19_01"],"award-info":[{"award-number":["TOPP_SID19_01"]}],"id":[{"id":"10.13039\/501100003500","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>G-quadruplexes (G4s) are non-canonical nucleic acid conformations that are widespread in all kingdoms of life and are emerging as important regulators both in RNA and DNA. Recently, two new higher-order architectures have been reported: adjacent interacting G4s and G4s with stable long loops forming stem-loop structures. As there are no specialized tools to identify these conformations, we developed QPARSE.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>QPARSE can exhaustively search for degenerate potential quadruplex-forming sequences (PQSs) containing bulges and\/or mismatches at genomic level, as well as either multimeric or long-looped PQS (MPQS and LLPQS, respectively). While its assessment versus known reference datasets is comparable with the state-of-the-art, what is more interesting is its performance in the identification of MPQS and LLPQS that present algorithms are not designed to search for. We report a comprehensive analysis of MPQS in human gene promoters and the analysis of LLPQS on three experimentally validated case studies from HIV-1, BCL2 and hTERT.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>QPARSE is freely accessible on the web at http:\/\/www.medcomp.medicina.unipd.it\/qparse\/index or downloadable from github as a python 2.7 program https:\/\/github.com\/B3rse\/qparse<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz569","type":"journal-article","created":{"date-parts":[[2019,7,16]],"date-time":"2019-07-16T19:13:43Z","timestamp":1563304423000},"page":"393-399","source":"Crossref","is-referenced-by-count":20,"title":["QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable"],"prefix":"10.1093","volume":"36","author":[{"given":"Michele","family":"Berselli","sequence":"first","affiliation":[{"name":"Department of Molecular Medicine, University of Padova , Padova I-35131, Italy"}]},{"given":"Enrico","family":"Lavezzo","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, University of Padova , Padova I-35131, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0246-3119","authenticated-orcid":false,"given":"Stefano","family":"Toppo","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, University of Padova , Padova I-35131, Italy"},{"name":"CRIBI Biotech Centre, University of Padova , Padova I-35131, Italy"}]}],"member":"286","published-online":{"date-parts":[[2019,7,22]]},"reference":[{"key":"2023013112082102800_btz569-B1","doi-asserted-by":"crossref","first-page":"W683","DOI":"10.1093\/nar\/gkl299","article-title":"Quadfinder: server for identification and analysis of quadruplex-forming motifs in nucleotide sequences","volume":"34","author":"Arora","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023013112082102800_btz569-B2","doi-asserted-by":"crossref","first-page":"429.","DOI":"10.3390\/molecules24030429","article-title":"Recent progress of targeted G-quadruplex-preferred ligands toward cancer therapy","volume":"24","author":"Asamitsu","year":"2019","journal-title":"Molecules"},{"key":"2023013112082102800_btz569-B3","doi-asserted-by":"crossref","first-page":"47411","DOI":"10.1074\/jbc.R400028200","article-title":"Non-B DNA conformations, genomic rearrangements, and human disease","volume":"279","author":"Bacolla","year":"2004","journal-title":"J. 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