{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T16:34:24Z","timestamp":1759336464854},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Conserved intron positions in eukaryotic genes can be used to reconstruct phylogenetic trees, to resolve ambiguous subfamily relationships in protein families and to infer the history of gene families. This version of GenePainter facilitates working with large datasets through options to select specific subsets for analysis and visualization, and through providing exhaustive statistics. GenePainter\u2019s application in phylogenetic analyses is considerably extended by the newly implemented integration of the exon\u2013intron pattern conservation with phylogenetic trees.<\/jats:p>\n               <jats:p>Availability and implementation: The software along with detailed documentation is available at http:\/\/www.motorprotein.de\/genepainter and as Supplementary Material.<\/jats:p>\n               <jats:p>Contact: \u00a0mako@nmr.mpibpc.mpg.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu798","type":"journal-article","created":{"date-parts":[[2014,12,1]],"date-time":"2014-12-01T01:08:52Z","timestamp":1417396132000},"page":"1302-1304","source":"Crossref","is-referenced-by-count":11,"title":["GenePainter v. 2.0 resolves the taxonomic distribution of intron positions"],"prefix":"10.1093","volume":"31","author":[{"given":"Stefanie","family":"M\u00fchlhausen","sequence":"first","affiliation":[{"name":"Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, G\u00f6ttingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcel","family":"Hellkamp","sequence":"additional","affiliation":[{"name":"Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, G\u00f6ttingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Kollmar","sequence":"additional","affiliation":[{"name":"Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, G\u00f6ttingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,11,29]]},"reference":[{"key":"2023051309021015400_btu798-B1","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/1745-6150-6-26","article-title":"A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes","volume":"6","author":"Chernikova","year":"2011","journal-title":"Biol. Direct"},{"key":"2023051309021015400_btu798-B2","first-page":"437","article-title":"Genome-wide identification and evolutionary and expression analyses of MYB-related genes in land plants","volume":"20","author":"Du","year":"2013","journal-title":"DNA Res. Int. J. Rapid Publ. Rep. Genes Genomes"},{"key":"2023051309021015400_btu798-B3","doi-asserted-by":"crossref","first-page":"1398","DOI":"10.1093\/bioinformatics\/bts153","article-title":"GECA: a fast tool for gene evolution and conservation analysis in eukaryotic protein families","volume":"28","author":"Fawal","year":"2012","journal-title":"Bioinformatics"},{"key":"2023051309021015400_btu798-B4","doi-asserted-by":"crossref","first-page":"D136","DOI":"10.1093\/nar\/gkr1178","article-title":"The NCBI taxonomy database","volume":"40","author":"Federhen","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023051309021015400_btu798-B5","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1471-2148-13-8","article-title":"Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes","volume":"13","author":"Grewe","year":"2013","journal-title":"BMC Evol. Biol."},{"key":"2023051309021015400_btu798-B7","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1186\/1471-2105-14-77","article-title":"GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures","volume":"14","author":"Hammesfahr","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023051309021015400_btu798-B8","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1002\/wrna.1143","article-title":"Whence genes in pieces: reconstruction of the exon-intron gene structures of the last eukaryotic common ancestor and other ancestral eukaryotes","volume":"4","author":"Koonin","year":"2013","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"2023051309021015400_btu798-B9","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1016\/j.ympev.2012.11.012","article-title":"Near intron pairs and the metazoan tree","volume":"66","author":"Lehmann","year":"2013","journal-title":"Mol. Phylogenet. Evol."},{"key":"2023051309021015400_btu798-B10","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1126\/science.1179302","article-title":"Extensive, recent intron gains in Daphnia populations","volume":"326","author":"Li","year":"2009","journal-title":"Science"},{"key":"2023051309021015400_btu798-B11","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1093\/nar\/28.1.85","article-title":"YIDB: the yeast intron database","volume":"28","author":"Lopez","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023051309021015400_btu798-B12","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/1471-2199-9-21","article-title":"Comparative genomic analysis of the arthropod muscle myosin heavy chain genes allows ancestral gene reconstruction and reveals a new type of \u2018partially\u2019 processed pseudogene","volume":"9","author":"Odronitz","year":"2008","journal-title":"BMC Mol. Biol."},{"key":"2023051309021015400_btu798-B13","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkn153","article-title":"Exalign: a new method for comparative analysis of exon\u2013intron gene structures","volume":"36","author":"Pavesi","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023051309021015400_btu798-B14","doi-asserted-by":"crossref","first-page":"1435","DOI":"10.1098\/rstb.2007.2233","article-title":"The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records","volume":"363","author":"Peterson","year":"2008","journal-title":"Philos. Trans. R. Soc. B Biol. Sci."},{"key":"2023051309021015400_btu798-B16","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1093\/bib\/bbp051","article-title":"Common introns within orthologous genes: software and application to plants","volume":"10","author":"Wilkerson","year":"2009","journal-title":"Brief. Bioinform."},{"key":"2023051309021015400_btu798-B17","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1007\/s00438-013-0786-0","article-title":"Evolution, functional divergence and conserved exon-intron structure of bHLH\/PAS gene family","volume":"289","author":"Yan","year":"2014","journal-title":"Mol. Genet. Genomics MGG"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/8\/1302\/50305914\/bioinformatics_31_8_1302.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/8\/1302\/50305914\/bioinformatics_31_8_1302.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,13]],"date-time":"2023-05-13T09:02:53Z","timestamp":1683968573000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/8\/1302\/212434"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,11,29]]},"references-count":15,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2015,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu798","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,4,15]]},"published":{"date-parts":[[2014,11,29]]}}}