{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T12:20:32Z","timestamp":1775737232520,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2016,10,3]],"date-time":"2016-10-03T00:00:00Z","timestamp":1475452800000},"content-version":"vor","delay-in-days":1371,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,1]]},"DOI":"10.1093\/database\/bat055","type":"journal-article","created":{"date-parts":[[2013,7,26]],"date-time":"2013-07-26T11:50:21Z","timestamp":1374839421000},"source":"Crossref","is-referenced-by-count":23,"title":["BmTEdb: a collective database of transposable elements in the silkworm genome"],"prefix":"10.1093","volume":"2013","author":[{"given":"Hong-En","family":"Xu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Silkworm Genome Biology, The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing 400716, China, 2Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 400044, China and 3College of Animal Science and Technology, Southwest University, Chongqing 400716, China"}]},{"given":"Hua-Hao","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Silkworm Genome Biology, The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing 400716, China, 2Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 400044, China and 3College of Animal Science and Technology, Southwest University, Chongqing 400716, China"}]},{"given":"Tian","family":"Xia","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Silkworm Genome Biology, The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing 400716, China, 2Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 400044, China and 3College of Animal Science and Technology, Southwest University, Chongqing 400716, China"}]},{"given":"Min-Jin","family":"Han","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Silkworm Genome Biology, The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing 400716, China, 2Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 400044, China and 3College of Animal Science and Technology, Southwest University, Chongqing 400716, China"}]},{"given":"Yi-Hong","family":"Shen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Silkworm Genome Biology, The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing 400716, China, 2Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 400044, China and 3College of Animal Science and Technology, Southwest University, Chongqing 400716, China"}]},{"given":"Ze","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Silkworm Genome Biology, The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing 400716, China, 2Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 400044, China and 3College of Animal Science and Technology, Southwest University, Chongqing 400716, China"}]}],"member":"286","published-online":{"date-parts":[[2013,7,25]]},"reference":[{"key":"key\n\t\t\t\t20180618192001_bat055-B1","first-page":"31","article-title":"Computational analysis and paleogenomics of interspersed repeats in eukaryotes","volume-title":"Computational Genomics: Current Methods","author":"Feschotte","year":"2007"},{"key":"key\n\t\t\t\t20180618192001_bat055-B2","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/0168-9525(89)90039-5","article-title":"Eukaryotic transposable elements and genome evolution","volume":"5","author":"Finnegan","year":"1989","journal-title":"Trends Genet."},{"key":"key\n\t\t\t\t20180618192001_bat055-B3","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1038\/nrg2165","article-title":"A unified classification system for eukaryotic transposable elements","volume":"8","author":"Wicker","year":"2007","journal-title":"Nat. Rev. Genet."},{"key":"key\n\t\t\t\t20180618192001_bat055-B4","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/S0378-1119(97)00409-5","article-title":"SINEs and LINEs share common 3\u2032 sequences: a review","volume":"205","author":"Okada","year":"1997","journal-title":"Gene"},{"key":"key\n\t\t\t\t20180618192001_bat055-B5","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1146\/annurev.genet.40.110405.090448","article-title":"DNA transposons and the evolution of eukaryotic genomes","volume":"41","author":"Feschotte","year":"2007","journal-title":"Annu. Rev. Genet."},{"key":"key\n\t\t\t\t20180618192001_bat055-B6","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1038\/nrg2337","article-title":"Transposable elements and the evolution of regulatory networks","volume":"9","author":"Feschotte","year":"2008","journal-title":"Nat. Rev. Genet."},{"key":"key\n\t\t\t\t20180618192001_bat055-B7","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1093\/bib\/bbm048","article-title":"Discovering and detecting transposable elements in genome sequences","volume":"8","author":"Bergman","year":"2007","journal-title":"Brief. Bioinform."},{"key":"key\n\t\t\t\t20180618192001_bat055-B8","doi-asserted-by":"crossref","first-page":"3391","DOI":"10.1021\/cr0683008","article-title":"Genome assembly, rearrangement, and repeats","volume":"38","author":"Tang","year":"2007","journal-title":"Chem. Rev."},{"key":"key\n\t\t\t\t20180618192001_bat055-B9","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/nrg2165-c3","article-title":"A unified classification system for eukaryotic transposable elements should reflect their phylogeny","volume":"10","author":"Seberg","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"key\n\t\t\t\t20180618192001_bat055-B10","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nrg2165-c1","article-title":"A universal classification of eukaryotic transposable elements implemented in Repbase","volume":"9","author":"Kapitonov","year":"2008","journal-title":"Nat. Rev. Genet."},{"key":"key\n\t\t\t\t20180618192001_bat055-B11","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1038\/hdy.2009.165","article-title":"Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs","volume":"104","author":"Lerat","year":"2009","journal-title":"Heredity (Edinb)"},{"key":"key\n\t\t\t\t20180618192001_bat055-B12","doi-asserted-by":"crossref","first-page":"1937","DOI":"10.1126\/science.1102210","article-title":"A draft sequence for the genome of the domesticated silkworm (Bombyx mori)","volume":"306","author":"Xia","year":"2004","journal-title":"Science"},{"key":"key\n\t\t\t\t20180618192001_bat055-B13","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.1016\/j.ibmb.2008.05.012","article-title":"Genome-wide screening and characterization of transposable elements and their distribution analysis in the silkworm, Bombyx mori","volume":"38","author":"Osanai-Futahashi","year":"2008","journal-title":"Insect Biochem. Mol. Biol."},{"key":"key\n\t\t\t\t20180618192001_bat055-B14","doi-asserted-by":"crossref","first-page":"e43","DOI":"10.1371\/journal.pcbi.0010043","article-title":"ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun","volume":"1","author":"Li","year":"2005","journal-title":"PLoS Comp. Biol."},{"key":"key\n\t\t\t\t20180618192001_bat055-B15","doi-asserted-by":"crossref","first-page":"1036","DOI":"10.1016\/j.ibmb.2008.11.004","article-title":"The genome of a lepidopteran model insect, the silkworm Bombyx mori","volume":"38","author":"Xia","year":"2008","journal-title":"Insect Biochem. Mol. Biol."},{"key":"key\n\t\t\t\t20180618192001_bat055-B16","doi-asserted-by":"crossref","first-page":"D453","DOI":"10.1093\/nar\/gkp801","article-title":"SilkDB v2.0: a platform for silkworm (Bombyx mori) genome biology","volume":"38","author":"Duan","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618192001_bat055-B17","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1186\/1471-2164-10-486","article-title":"KAIKObase: An integrated silkworm genome database and data mining tool","volume":"10","author":"Shimomura","year":"2009","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20180618192001_bat055-B18","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1159\/000084979","article-title":"Repbase Update, a database of eukaryotic repetitive elements","volume":"110","author":"Jurka","year":"2005","journal-title":"Cytogenet. Genome Res."},{"key":"key\n\t\t\t\t20180618192001_bat055-B19","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1186\/1471-2164-11-520","article-title":"Burst expansion, distribution and diversification of MITEs in the silkworm genome","volume":"11","author":"Han","year":"2010","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20180618192001_bat055-B20","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/S1673-8527(09)60031-X","article-title":"BmSE, a SINE family with 3\u2032 ends of (ATTT) repeats in domesticated silkworm (Bombyx mori)","volume":"37","author":"Xu","year":"2010","journal-title":"J Genet Genomics"},{"key":"key\n\t\t\t\t20180618192001_bat055-B21","article-title":"Identification and fuction analysis of short interspersed repetitive sequence (BmSer_SINE) of silkworm, Bombyx mori. Ph.D Thesis","author":"Huang","year":"2009"},{"key":"key\n\t\t\t\t20180618192001_bat055-B22","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1093\/bioinformatics\/btf878","article-title":"LTR_STRUC: a novel search and identification program for LTR retrotransposons","volume":"19","author":"McCarthy","year":"2003","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180618192001_bat055-B23","doi-asserted-by":"crossref","first-page":"W265","DOI":"10.1093\/nar\/gkm286","article-title":"LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons","volume":"35","author":"Xu","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618192001_bat055-B24","doi-asserted-by":"crossref","first-page":"e143","DOI":"10.1093\/nar\/gkp752","article-title":"MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes","volume":"37","author":"Rho","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618192001_bat055-B25","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1016\/j.ibmb.2005.03.014","article-title":"Survey of long terminal repeat retrotransposons of domesticated silkworm (Bombyx mori)","volume":"35","author":"Xu","year":"2005","journal-title":"Insect Biochem. Mol. Biol."},{"key":"key\n\t\t\t\t20180618192001_bat055-B26","first-page":"1","article-title":"FastPCR software for PCR primer and probe design and repeat search","volume":"3","author":"Kalendar","year":"2009","journal-title":"Genes Genomes Genomics"},{"key":"key\n\t\t\t\t20180618192001_bat055-B27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.gene.2006.09.011","article-title":"Improved repeat identification and masking in Dipterans","volume":"389","author":"Smith","year":"2007","journal-title":"Gene"},{"key":"key\n\t\t\t\t20180618192001_bat055-B28","doi-asserted-by":"crossref","first-page":"i152","DOI":"10.1093\/bioinformatics\/bti1003","article-title":"PILER: identification and classification of genomic repeats","volume":"21","author":"Edgar","year":"2005","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180618192001_bat055-B29","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/nar\/27.2.573","article-title":"Tandem repeats finder: a program to analyze DNA sequences","volume":"27","author":"Benson","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618192001_bat055-B30","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1186\/1471-2105-7-474","article-title":"Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor","volume":"7","author":"Kohany","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180618192001_bat055-B31","doi-asserted-by":"crossref","first-page":"1329","DOI":"10.1093\/bioinformatics\/btp084","article-title":"TEclass\u2014a tool for automated classification of unknown eukaryotic transposable elements","volume":"25","author":"Abrusan","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180618192001_bat055-B32","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618192001_bat055-B33","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","article-title":"EMBOSS: the European Molecular Biology Open Software Suite","volume":"16","author":"Rice","year":"2000","journal-title":"Trends Genet."},{"key":"key\n\t\t\t\t20180618192001_bat055-B34","doi-asserted-by":"crossref","first-page":"W29","DOI":"10.1093\/nar\/gkr367","article-title":"HMMER web server: interactive sequence similarity searching","volume":"39","author":"Finn","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618192001_bat055-B35","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1186\/1471-2164-8-90","article-title":"De novo identification of LTR retrotransposons in eukaryotic genomes","volume":"8","author":"Rho","year":"2007","journal-title":"BMC Genomics"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/bat055\/11197785\/bat055.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,7,19]],"date-time":"2019-07-19T17:10:56Z","timestamp":1563556256000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/bat055\/338897"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,1,1]]},"references-count":35,"URL":"https:\/\/doi.org\/10.1093\/database\/bat055","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2013]]},"published":{"date-parts":[[2013,1,1]]}}}