{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,5]],"date-time":"2023-09-05T05:06:13Z","timestamp":1693890373246},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Inversions are a common form of structural variation, which may have a marked effect on the genome and methods to infer quantities of interest such as those relating to population structure and natural selection. However, due to the challenge in detecting inversions, little is presently known about their impact. Software to simulate inversions could be used to provide a better understanding of how to detect and account for them; but while there are several software packages for simulating population genetic data, none incorporate inversion polymorphisms. Here, we describe a software package, modified from the forward-in-time simulator FREGENE, which simulates the evolution of an inversion polymorphism, of specified length, location, frequency and age, in a population of sequences. We describe previously unreported signatures of inversions in SNP data observed in invertFREGENE results and a known inversion in humans.<\/jats:p>\n               <jats:p>Availability: C++ source code and user manual are available for download from http:\/\/www.ebi.ac.uk\/projects\/BARGEN\/ under the GPL licence.<\/jats:p>\n               <jats:p>Contact: \u00a0l.coin@ic.ac.uk; c.hoggart@ic.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq029","type":"journal-article","created":{"date-parts":[[2010,1,28]],"date-time":"2010-01-28T01:13:21Z","timestamp":1264641201000},"page":"838-840","source":"Crossref","is-referenced-by-count":11,"title":["invertFREGENE: software for simulating inversions in population genetic data"],"prefix":"10.1093","volume":"26","author":[{"given":"Paul F.","family":"O'Reilly","sequence":"first","affiliation":[{"name":"Department of Epidemiology and Biostatistics, Imperial College"}]},{"given":"Lachlan J. M.","family":"Coin","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics, Imperial College"}]},{"given":"Clive J.","family":"Hoggart","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics, Imperial College"}]}],"member":"286","published-online":{"date-parts":[[2010,1,26]]},"reference":[{"key":"2023012508013831400_B1","doi-asserted-by":"crossref","first-page":"2555","DOI":"10.1093\/hmg\/ddp187","article-title":"Characterization of six human disease-associated inversion polymorphisms","volume":"18","author":"Antonaccil","year":"2007","journal-title":"Hum. Mol. Genet."},{"key":"2023012508013831400_B2","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1101\/gr.5774507","article-title":"Evidence for large inversion polymorphisms in the human genome from HapMap data","volume":"17","author":"Bansal","year":"2007","journal-title":"Genome Res."},{"key":"2023012508013831400_B3","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1093\/bioinformatics\/bth457","article-title":"Haploview: analysis and visualization of LD and haplotype maps","volume":"21","author":"Barrett","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012508013831400_B4","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1186\/1471-2105-9-364","article-title":"Fregene: simulation of realistic sequence-level data in populations and ascertained samples","volume":"9","author":"Chadeau-Hyam","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012508013831400_B5","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1002\/humu.20775","article-title":"An unusual haplotype structure on human chromosome 8p23 derived from the inversion polymorphism","volume":"29","author":"Deng","year":"2008","journal-title":"Hum. Mut."},{"key":"2023012508013831400_B6","doi-asserted-by":"crossref","first-page":"1725","DOI":"10.1534\/genetics.106.069088","article-title":"Sequence-level population simulations over large genomic regions","volume":"177","author":"Hoggart","year":"2007","journal-title":"Genetics"},{"key":"2023012508013831400_B7","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature06862","article-title":"Mapping and sequencing of structural variation from eight human genomes","volume":"453","author":"Kidd","year":"2008","journal-title":"Nature"},{"key":"2023012508013831400_B8","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1093\/genetics\/155.2.685","article-title":"Effect of inversion polymorphism on the neutral nucleotide variability of linked chromosomal regions in Drosophila","volume":"155","author":"Navarro","year":"2000","journal-title":"Genetics"},{"key":"2023012508013831400_B9","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/j.ajhg.2008.06.005","article-title":"Long-range LD can confound genome scans in admixed populations","volume":"83","author":"Price","year":"2008","journal-title":"Am. J. Hum. Genet."},{"key":"2023012508013831400_B10","doi-asserted-by":"crossref","first-page":"1576","DOI":"10.1101\/gr.3709305","article-title":"Calibrating a coalescent simulation of human genome sequence variation","volume":"15","author":"Schaffner","year":"2005","journal-title":"Genome Res."},{"key":"2023012508013831400_B11","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1146\/annurev.genom.7.080505.115618","article-title":"Structural variation of the human genome","volume":"7","author":"Sharp","year":"2006","journal-title":"Ann. Rev. Genomics Hum. Genet."},{"key":"2023012508013831400_B12","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1093\/hmg\/ddm016","article-title":"Characterization of a recurrent 15q24 microdeletion syndrome","volume":"16","author":"Sharp","year":"2007","journal-title":"Hum. Mol. Genet."},{"key":"2023012508013831400_B13","first-page":"418","article-title":"Identification and frequency estimation of inversion polymorphisms from haplotype data","volume":"5541","author":"Sindi","year":"2009","journal-title":"RECOMB"},{"key":"2023012508013831400_B14","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1038\/ng1508","article-title":"A common inversion under selection in Europeans","volume":"37","author":"Stefansson","year":"2005","journal-title":"Nat. Genet."},{"key":"2023012508013831400_B15","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1038\/nature06258","article-title":"A second generation human haplotype map of over 3.1 million SNPs","volume":"449","author":"The International HapMap Consortium","year":"2007","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/6\/838\/48854832\/bioinformatics_26_6_838.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/6\/838\/48854832\/bioinformatics_26_6_838.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:01:54Z","timestamp":1674633714000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/6\/838\/244528"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,1,26]]},"references-count":15,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2010,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq029","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,3,15]]},"published":{"date-parts":[[2010,1,26]]}}}