{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T21:47:24Z","timestamp":1772228844278,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2018,7,7]],"date-time":"2018-07-07T00:00:00Z","timestamp":1530921600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,15]]},"abstract":"Abstract<\/jats:title>\n \n Summary<\/jats:title>\n Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs which guide endonucleases to mRNAs of actively transcribed transposons in order to prevent their translation. The resulting mRNA fragments induce a positive feedback loop (the \u2018ping-pong cycle\u2019), which reinforces piRNA production and hence the transposon-silencing effect. PingPongPro is a command-line tool to scan small RNA-Seq data for signs of ping-pong cycle activity. It implements a novel algorithm that combines empirical probabilities in a multi-factor model to accurately identify transposons which are suppressed through the ping-pong cycle.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n Source code, a user manual, and binaries for Microsoft Windows and Linux are available at https:\/\/github.com\/suhrig\/pingpongpro under the GPLv3 license.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty578","type":"journal-article","created":{"date-parts":[[2018,7,4]],"date-time":"2018-07-04T19:39:34Z","timestamp":1530733174000},"page":"335-336","source":"Crossref","is-referenced-by-count":24,"title":["PingPongPro: a tool for the detection of piRNA-mediated transposon-silencing in small RNA-Seq data"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0068-5957","authenticated-orcid":false,"given":"Sebastian","family":"Uhrig","sequence":"first","affiliation":[{"name":"Bioinformatics Core Facility, Institute of Molecular Biology, Mainz, Germany"}]},{"given":"Holger","family":"Klein","sequence":"additional","affiliation":[{"name":"Bioinformatics Core Facility, Institute of Molecular Biology, Mainz, Germany"},{"name":"Computational Biology Group, Target Discovery Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Ri\u00df, Deutschland"}]}],"member":"286","published-online":{"date-parts":[[2018,7,7]]},"reference":[{"key":"2023013107232599100_bty578-B1","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1007\/978-1-4939-0931-5_12","article-title":"Computing siRNA and piRNA overlap signatures","volume":"1173","author":"Antoniewski","year":"2014","journal-title":"Methods Mol. Biol"},{"key":"2023013107232599100_bty578-B2","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1016\/j.cell.2007.01.043","article-title":"Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila","volume":"128","author":"Brennecke","year":"2007","journal-title":"Cell"},{"key":"2023013107232599100_bty578-B3","doi-asserted-by":"crossref","first-page":"11.","DOI":"10.1186\/1471-2105-9-11","article-title":"SeqAn an efficient, generic C++ library for sequence analysis","volume":"9","author":"D\u00f6ring","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023013107232599100_bty578-B4","doi-asserted-by":"crossref","first-page":"1587","DOI":"10.1126\/science.1140494","article-title":"A slicer-mediated mechanism for repeat-associated siRNA 5' end formation in Drosophila","volume":"315","author":"Gunawardane","year":"2007","journal-title":"Science"},{"key":"2023013107232599100_bty578-B5","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/bioinformatics\/btu647","article-title":"piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing","volume":"31","author":"Han","year":"2015","journal-title":"Bioinformatics"},{"key":"2023013107232599100_bty578-B6","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1016\/j.cell.2009.04.027","article-title":"Without Argonaute3, Aubergine-bound piRNAs collapse but Piwi-bound piRNAs persist","volume":"137","author":"Li","year":"2009","journal-title":"Cell"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/2\/335\/48963541\/bioinformatics_35_2_335.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/2\/335\/48963541\/bioinformatics_35_2_335.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T09:54:00Z","timestamp":1675158840000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/2\/335\/5050396"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,7,7]]},"references-count":6,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2019,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty578","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,1,15]]},"published":{"date-parts":[[2018,7,7]]}}}