{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T08:26:15Z","timestamp":1773476775561,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We present MASiVE, an expertly built tool for the large-scale, yet sensitive and highly accurate, discovery, preliminary analysis and insertion age estimation of intact Sirevirus LTR-retrotransposons in plant genomic sequences. Validation was based on the recently available and annotated large maize chromosome one. Results show a considerable improvement in the annotation of Sireviruses, and support our approach as an important addition to the bioinformatics toolbox of plant biologists.<\/jats:p>\n               <jats:p>Availability: PERL source code and essential files are available online at http:\/\/bat.ina.certh.gr\/tools\/masive\/. The freely available Vmatch, LTRharvest, Wise2, and MAFFT algorithms are required.<\/jats:p>\n               <jats:p>Contact: \u00a0ndarz@certh.gr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq454","type":"journal-article","created":{"date-parts":[[2010,8,10]],"date-time":"2010-08-10T02:04:44Z","timestamp":1281405884000},"page":"2452-2454","source":"Crossref","is-referenced-by-count":21,"title":["MASiVE: Mapping and Analysis of SireVirus Elements in plant genome sequences"],"prefix":"10.1093","volume":"26","author":[{"given":"N.","family":"Darzentas","sequence":"first","affiliation":[{"name":"1 Institute of Agrobiotechnology, Centre for Research and Technology Hellas, Thessaloniki 57001 and 2Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki, Thessaloniki 54006, Greece"}]},{"given":"A.","family":"Bousios","sequence":"additional","affiliation":[{"name":"1 Institute of Agrobiotechnology, Centre for Research and Technology Hellas, Thessaloniki 57001 and 2Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki, Thessaloniki 54006, Greece"}]},{"given":"V.","family":"Apostolidou","sequence":"additional","affiliation":[{"name":"1 Institute of Agrobiotechnology, Centre for Research and Technology Hellas, Thessaloniki 57001 and 2Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki, Thessaloniki 54006, Greece"}]},{"given":"A. S.","family":"Tsaftaris","sequence":"additional","affiliation":[{"name":"1 Institute of Agrobiotechnology, Centre for Research and Technology Hellas, Thessaloniki 57001 and 2Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki, Thessaloniki 54006, Greece"},{"name":"1 Institute of Agrobiotechnology, Centre for Research and Technology Hellas, Thessaloniki 57001 and 2Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki, Thessaloniki 54006, Greece"}]}],"member":"286","published-online":{"date-parts":[[2010,8,9]]},"reference":[{"key":"2023012508170848500_B1","doi-asserted-by":"crossref","first-page":"e1000732","DOI":"10.1371\/journal.pgen.1000732","article-title":"Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome","volume":"5","author":"Baucom","year":"2009","journal-title":"Plos Genet."},{"key":"2023012508170848500_B2","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1101\/gr.1865504","article-title":"Genewise and genomewise","volume":"14","author":"Birney","year":"2004","journal-title":"Genome Res."},{"key":"2023012508170848500_B3","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1186\/1471-2164-11-89","article-title":"Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants?","volume":"11","author":"Bousios","year":"2010","journal-title":"BMC Genomics"},{"key":"2023012508170848500_B4","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/1471-2105-9-18","article-title":"LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons","volume":"9","author":"Ellinghaus","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012508170848500_B5","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1093\/bib\/bbn013","article-title":"Recent developments in the MAFFT multiple sequence alignment program","volume":"9","author":"Katoh","year":"2008","journal-title":"Brief. 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