{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T18:36:37Z","timestamp":1776710197815,"version":"3.51.2"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Developmental DNA elimination occurs in a wide variety of multicellular organisms, but ciliates are the only single-celled eukaryotes in which this phenomenon has been reported. Despite considerable interest in ciliates as models for DNA elimination, no standard methods for identification and characterization of the eliminated sequences are currently available.<\/jats:p>\n               <jats:p>Results: We present the Paramecium Toolbox for Interspersed DNA Elimination Studies (ParTIES), designed for Paramecium species, that (i) identifies eliminated sequences, (ii) measures their presence in a sequencing sample and (iii) detects rare elimination polymorphisms.<\/jats:p>\n               <jats:p>Availability and implementation: ParTIES is multi-threaded Perl software available at https:\/\/github.com\/oarnaiz\/ParTIES. ParTIES is distributed under the GNU General Public Licence v3.<\/jats:p>\n               <jats:p>Contact: \u00a0linda.sperling@i2bc.paris-saclay.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv691","type":"journal-article","created":{"date-parts":[[2015,11,21]],"date-time":"2015-11-21T02:29:46Z","timestamp":1448072986000},"page":"599-601","source":"Crossref","is-referenced-by-count":46,"title":["ParTIES: a toolbox for <i>Paramecium<\/i> interspersed DNA elimination studies"],"prefix":"10.1093","volume":"32","author":[{"given":"Cyril","family":"Denby Wilkes","sequence":"first","affiliation":[{"name":"Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Universit\u00e9 Paris-Saclay, 91198, Gif-sur-Yvette cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olivier","family":"Arnaiz","sequence":"additional","affiliation":[{"name":"Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Universit\u00e9 Paris-Saclay, 91198, Gif-sur-Yvette cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Linda","family":"Sperling","sequence":"additional","affiliation":[{"name":"Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Universit\u00e9 Paris-Saclay, 91198, Gif-sur-Yvette cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,11,20]]},"reference":[{"key":"2023020110351018600_btv691-B1","doi-asserted-by":"crossref","first-page":"e1002984","DOI":"10.1371\/journal.pgen.1002984","article-title":"The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences","volume":"8","author":"Arnaiz","year":"2012","journal-title":"PLoS Genet."},{"key":"2023020110351018600_btv691-B2","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/nature05230","article-title":"Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia","volume":"444","author":"Aury","year":"2006","journal-title":"Nature"},{"key":"2023020110351018600_btv691-B3","doi-asserted-by":"crossref","first-page":"2478","DOI":"10.1101\/gad.547309","article-title":"PiggyMac: a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraurelia","volume":"23","author":"Baudry","year":"2009","journal-title":"Genes Dev."},{"key":"2023020110351018600_btv691-B4","doi-asserted-by":"crossref","first-page":"e1001518","DOI":"10.1371\/journal.pbio.1001518","article-title":"Selecting one of several mating types through gene segment joining and deletion in Tetrahymena thermophila","volume":"11","author":"Cervantes","year":"2013","journal-title":"PLoS Biol."},{"key":"2023020110351018600_btv691-B5","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1016\/j.cell.2014.07.034","article-title":"The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development","volume":"158","author":"Chen","year":"2014","journal-title":"Cell"},{"key":"2023020110351018600_btv691-B6","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1101\/gr.074534.107","article-title":"Analysis of sequence variability in the macronuclear DNA of paramecium tetraurelia: a somatic view of the germline","volume":"18","author":"Duret","year":"2008","journal-title":"Genome Res."},{"key":"2023020110351018600_btv691-B7","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1101\/gad.473008","article-title":"Maternal noncoding transcripts antagonize the targeting of DNA elimination by scanRNAs in Paramecium tetraurelia","volume":"22","author":"Lep\u00e8re","year":"2008","journal-title":"Genes Dev."},{"key":"2023020110351018600_btv691-B8","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1093\/nar\/gkn1018","article-title":"Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia","volume":"37","author":"Lep\u00e8re","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023020110351018600_btv691-B9","doi-asserted-by":"crossref","first-page":"22140","DOI":"10.1073\/pnas.1012236107","article-title":"RNA-mediated epigenetic regulation of DNA copy number","volume":"107","author":"Nowacki","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2023020110351018600_btv691-B10","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1038\/nature13318","article-title":"Genome-defence small RNAs exapted for epigenetic mating-type inheritance","volume":"509","author":"Singh","year":"2014","journal-title":"Nature"},{"key":"2023020110351018600_btv691-B11","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.gde.2014.03.012","article-title":"Programmed DNA elimination in multicellular organisms","volume":"27","author":"Wang","year":"2014","journal-title":"Curr. Opin. Genet. Dev."},{"key":"2023020110351018600_btv691-B12","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: algorithms for de novo short read assembly using de Bruijn graphs","volume":"18","author":"Zerbino","year":"2008","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/4\/599\/49017591\/bioinformatics_32_4_599.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/4\/599\/49017591\/bioinformatics_32_4_599.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T21:58:13Z","timestamp":1675288693000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/4\/599\/1744483"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,11,20]]},"references-count":12,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2016,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv691","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,2,15]]},"published":{"date-parts":[[2015,11,20]]}}}