{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T08:48:20Z","timestamp":1769590100351,"version":"3.49.0"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Upgrade and integration of triplex software into the R\/Bioconductor framework.<\/jats:p>\n               <jats:p>Results: We combined a previously published implementation of a triplex DNA search algorithm with visualization to create a versatile R\/Bioconductor package \u2018triplex\u2019. The new package provides functions that can be used to search Bioconductor genomes and other DNA sequence data for occurrence of nucleotide patterns capable of forming intramolecular triplexes (H-DNA). Functions producing 2D and 3D diagrams of the identified triplexes allow instant visualization of the search results. Leveraging the power of Biostrings and GRanges classes, the results get fully integrated into the existing Bioconductor framework, allowing their passage to other Genome visualization and annotation packages, such as GenomeGraphs, rtracklayer or Gviz.<\/jats:p>\n               <jats:p>Availability: R package \u2018triplex\u2019 is available from Bioconductor (bioconductor.org).<\/jats:p>\n               <jats:p>Contact: \u00a0lexa@fi.muni.cz<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt299","type":"journal-article","created":{"date-parts":[[2013,5,25]],"date-time":"2013-05-25T03:49:30Z","timestamp":1369453770000},"page":"1900-1901","source":"Crossref","is-referenced-by-count":30,"title":["Triplex: an R\/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences"],"prefix":"10.1093","volume":"29","author":[{"given":"Ji\u0159\u00ed","family":"Hon","sequence":"first","affiliation":[{"name":"1 Department of Computer Systems, Faculty of Information Technology, Brno Technical University, Bo\u017eet\u011bchova 2, 61266 Brno and 2Department of Information Technology, Faculty of Informatics, Masaryk University, Botanick\u00e1 68a, 60200 Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tom\u00e1\u0161","family":"Mart\u00ednek","sequence":"additional","affiliation":[{"name":"1 Department of Computer Systems, Faculty of Information Technology, Brno Technical University, Bo\u017eet\u011bchova 2, 61266 Brno and 2Department of Information Technology, Faculty of Informatics, Masaryk University, Botanick\u00e1 68a, 60200 Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kamil","family":"Rajdl","sequence":"additional","affiliation":[{"name":"1 Department of Computer Systems, Faculty of Information Technology, Brno Technical University, Bo\u017eet\u011bchova 2, 61266 Brno and 2Department of Information Technology, Faculty of Informatics, Masaryk University, Botanick\u00e1 68a, 60200 Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matej","family":"Lexa","sequence":"additional","affiliation":[{"name":"1 Department of Computer Systems, Faculty of Information Technology, Brno Technical University, Bo\u017eet\u011bchova 2, 61266 Brno and 2Department of Information Technology, Faculty of Informatics, Masaryk University, Botanick\u00e1 68a, 60200 Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,5,24]]},"reference":[{"key":"2023012810450010500_btt299-B1","doi-asserted-by":"crossref","first-page":"1372","DOI":"10.1101\/gr.130237.111","article-title":"Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic","volume":"22","author":"Buske","year":"2012","journal-title":"Genome Res."},{"key":"2023012810450010500_btt299-B2","doi-asserted-by":"crossref","DOI":"10.1002\/0471142905.hg1807s73","volume-title":"Searching for Non-B DNA-Forming Motifs Using nBMST (Non-B DNA Motif Search Tool)","author":"Cer","year":"2012"},{"key":"2023012810450010500_btt299-B3","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1006\/jmbi.2000.4502","article-title":"Searching genomes for sequences with the potential to form intrastrand triple helices","volume":"302","author":"Hoyne","year":"2000","journal-title":"J. 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USA"},{"key":"2023012810450010500_btt299-B7","volume-title":"Triple-Helical Nucleic Acids","author":"Soyfer","year":"1995"},{"key":"2023012810450010500_btt299-B8","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1002\/jmr.528","article-title":"Evidence for a DNA triplex in a recombination-like motif: I. recognition of Watson-Crick base pairs by natural bases in a high-stability triplex","volume":"14","author":"Walter","year":"2001","journal-title":"J. Mol. 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