{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T04:41:43Z","timestamp":1780461703361,"version":"3.54.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: i-ADHoRe is a software tool that combines gene content and gene order information of homologous genomic segments into profiles to detect highly degenerated homology relations within and between genomes. The new version offers, besides a significant increase in performance, several optimizations to the algorithm, most importantly to the profile alignment routine. As a result, the annotations of multiple genomes, or parts thereof, can be fed simultaneously into the program, after which it will report all regions of homology, both within and between genomes.<\/jats:p>\n               <jats:p>Availability: The i-ADHoRe 2.0 package contains the C++ source code for the main program as well as various Perl scripts and a fully documented Perl API to facilitate post-processing. The software runs on any Linux- or -UNIX based platform. The package is freely available for academic users and can be downloaded from http:\/\/bioinformatics.psb.ugent.be\/<\/jats:p>\n               <jats:p>Contact: \u00a0yves.vandepeer@psb.ugent.be<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm449","type":"journal-article","created":{"date-parts":[[2007,10,19]],"date-time":"2007-10-19T00:25:26Z","timestamp":1192753526000},"page":"127-128","source":"Crossref","is-referenced-by-count":39,"title":["i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles"],"prefix":"10.1093","volume":"24","author":[{"given":"Cedric","family":"Simillion","sequence":"first","affiliation":[{"name":"1 Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University, Newcastle-upon-Tyne, UK, 2Departement Industri\u00eble Wetenschappen BME-CTL, Hogeschool Gent, B-9000 Ghent, 3Department of Plant Systems Biology, VIB and 4Bioinformatics and Evolutionary Genomics, Department of Molecular Genetics, Ghent University, B-9052 Ghent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Koen","family":"Janssens","sequence":"additional","affiliation":[{"name":"1 Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University, Newcastle-upon-Tyne, UK, 2Departement Industri\u00eble Wetenschappen BME-CTL, Hogeschool Gent, B-9000 Ghent, 3Department of Plant Systems Biology, VIB and 4Bioinformatics and Evolutionary Genomics, Department of Molecular Genetics, Ghent University, B-9052 Ghent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lieven","family":"Sterck","sequence":"additional","affiliation":[{"name":"1 Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University, Newcastle-upon-Tyne, UK, 2Departement Industri\u00eble Wetenschappen BME-CTL, Hogeschool Gent, B-9000 Ghent, 3Department of Plant Systems Biology, VIB and 4Bioinformatics and Evolutionary Genomics, Department of Molecular Genetics, Ghent University, B-9052 Ghent, Belgium"},{"name":"1 Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University, Newcastle-upon-Tyne, UK, 2Departement Industri\u00eble Wetenschappen BME-CTL, Hogeschool Gent, B-9000 Ghent, 3Department of Plant Systems Biology, VIB and 4Bioinformatics and Evolutionary Genomics, Department of Molecular Genetics, Ghent University, B-9052 Ghent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yves","family":"Van de Peer","sequence":"additional","affiliation":[{"name":"1 Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University, Newcastle-upon-Tyne, UK, 2Departement Industri\u00eble Wetenschappen BME-CTL, Hogeschool Gent, B-9000 Ghent, 3Department of Plant Systems Biology, VIB and 4Bioinformatics and Evolutionary Genomics, Department of Molecular Genetics, Ghent University, B-9052 Ghent, Belgium"},{"name":"1 Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University, Newcastle-upon-Tyne, UK, 2Departement Industri\u00eble Wetenschappen BME-CTL, Hogeschool Gent, B-9000 Ghent, 3Department of Plant Systems Biology, VIB and 4Bioinformatics and Evolutionary Genomics, Department of Molecular Genetics, Ghent University, B-9052 Ghent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2007,10,17]]},"reference":[{"key":"2023020209443687500_B1","doi-asserted-by":"crossref","first-page":"14959","DOI":"10.1073\/pnas.0603228103","article-title":"Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes","volume":"103","author":"Cannon","year":"2006","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020209443687500_B2","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1126\/science.1095781","article-title":"The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome","volume":"304","author":"Dietrich","year":"2004","journal-title":"Science"},{"key":"2023020209443687500_B3","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1038\/nature02579","article-title":"Genome evolution in yeasts","volume":"430","author":"Dujon","year":"2004","journal-title":"Nature"},{"key":"2023020209443687500_B4","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1038\/nature02424","article-title":"Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae","volume":"428","author":"Kellis","year":"2004","journal-title":"Nature"},{"key":"2023020209443687500_B5","doi-asserted-by":"crossref","first-page":"7705","DOI":"10.1073\/pnas.0611046104","article-title":"The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation","volume":"104","author":"Palenik","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020209443687500_B6","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1101\/gr.2179004","article-title":"Building genomic profiles for uncovering segmental homology in the twilight zone","volume":"14","author":"Simillion","year":"2004","journal-title":"Genome Res"},{"key":"2023020209443687500_B7","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1002\/bies.20127","article-title":"Recent developments in computational approaches for uncovering genomic homology","volume":"26","author":"Simillion","year":"2004","journal-title":"Bioessays"},{"key":"2023020209443687500_B8","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1016\/S0168-9525(02)02796-8","article-title":"Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice","volume":"18","author":"Vandepoele","year":"2002","journal-title":"Trends Genet"},{"key":"2023020209443687500_B9","doi-asserted-by":"crossref","first-page":"299","DOI":"10.2174\/1389202043349237","article-title":"The quest for genomic homology","volume":"5","author":"Vandepoele","year":"2004","journal-title":"Curr. Genomics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/1\/127\/49043964\/bioinformatics_24_1_127.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/1\/127\/49043964\/bioinformatics_24_1_127.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T10:05:12Z","timestamp":1675332312000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/1\/127\/204920"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,10,17]]},"references-count":9,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm449","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,1,1]]},"published":{"date-parts":[[2007,10,17]]}}}