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for chromosomal rearrangements that include disease-causing deletions, inversions, and translocations. Comprehensive identification, classification and annotation of repeats in genomes can provide accurate and targeted solutions towards understanding and diagnosis of complex diseases, optimization of plant properties and development of new drugs. RepBase and Dfam are two most frequently used repeat databases, but they are not sufficiently complete. Due to the lack of a comprehensive repeat database of multiple species, the current research in this field is far from being satisfactory. LongRepMarker is a new framework developed recently by our group for comprehensive identification of genomic repeats. We here propose msRepDB based on LongRepMarker, which is currently the most comprehensive multi-species repeat database, covering &amp;gt;80 000 species. Comprehensive evaluations show that msRepDB contains more species, and more complete repeats and families than RepBase and Dfam databases. (https:\/\/msrepdb.cbrc.kaust.edu.sa\/pages\/msRepDB\/index.html).<\/jats:p>","DOI":"10.1093\/nar\/gkab1089","type":"journal-article","created":{"date-parts":[[2021,10,21]],"date-time":"2021-10-21T03:13:35Z","timestamp":1634786015000},"page":"D236-D245","source":"Crossref","is-referenced-by-count":22,"title":["msRepDB: a comprehensive repetitive sequence database of over 80 000 species"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0061-1317","authenticated-orcid":false,"given":"Xingyu","family":"Liao","sequence":"first","affiliation":[{"name":"Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia"},{"name":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China"}]},{"given":"Kang","family":"Hu","sequence":"additional","affiliation":[{"name":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China"}]},{"given":"Adil","family":"Salhi","sequence":"additional","affiliation":[{"name":"Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia"}]},{"given":"You","family":"Zou","sequence":"additional","affiliation":[{"name":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1516-0480","authenticated-orcid":false,"given":"Jianxin","family":"Wang","sequence":"additional","affiliation":[{"name":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7108-3574","authenticated-orcid":false,"given":"Xin","family":"Gao","sequence":"additional","affiliation":[{"name":"Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia"}]}],"member":"286","published-online":{"date-parts":[[2021,12,1]]},"reference":[{"key":"2022010507354211000_B1","doi-asserted-by":"crossref","first-page":"5237","DOI":"10.1073\/pnas.94.10.5237","article-title":"Characteristic enrichment of DNA repeats in different genomes","volume":"94","author":"Cox","year":"1997","journal-title":"Proc. Natl. Acad. Sci. 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Rev. Gen. Hum. Genet."},{"key":"2022010507354211000_B17","first-page":"28","article-title":"Transposable elements and human cancer: a causal relationship?","volume":"1835","author":"Ch\u00e9nais","year":"2013","journal-title":"Biochim. Biophys. Acta."},{"key":"2022010507354211000_B18","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1016\/j.semcancer.2010.06.001","article-title":"All y\u2019all need to know \u2019bout retroelements in cancer","volume":"20","author":"Belancio","year":"2010","journal-title":"Semin. Cancer Biol."},{"key":"2022010507354211000_B19","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s13100-015-0041-9","article-title":"Repbase update, a database of repetitive elements in eukaryotic genomes","volume":"6","author":"Bao","year":"2015","journal-title":"Mobile DNA"},{"key":"2022010507354211000_B20","doi-asserted-by":"crossref","first-page":"D81","DOI":"10.1093\/nar\/gkv1272","article-title":"The Dfam database of repetitive DNA families","volume":"44","author":"Hubley","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2022010507354211000_B21","doi-asserted-by":"crossref","first-page":"i351","DOI":"10.1093\/bioinformatics\/bti1018","article-title":"De novo identification of repeat families in large genomes","volume":"21","author":"Price","year":"2005","journal-title":"Bioinformatics"},{"key":"2022010507354211000_B22","first-page":"1996","volume-title":"RepeatMasker Open-4.0","author":"Smit","year":"2015"},{"key":"2022010507354211000_B23","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1038\/nature08670","article-title":"Genome sequence of the palaeopolyploid soybean","volume":"463","author":"Schmutz","year":"2010","journal-title":"Nature"},{"key":"2022010507354211000_B24","doi-asserted-by":"crossref","first-page":"e100","DOI":"10.1093\/nar\/gkab563","article-title":"A sensitive repeat identification framework based on short and long reads","volume":"49","author":"Liao","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507354211000_B25","doi-asserted-by":"crossref","first-page":"9451","DOI":"10.1073\/pnas.1921046117","article-title":"RepeatModeler2 for automated genomic discovery of transposable element families","volume":"117","author":"Jullien","year":"2020","journal-title":"Proc. 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Bioinformatics"},{"key":"2022010507354211000_B28","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1186\/s12859-018-2336-6","article-title":"Rapid and precise alignment of raw reads against redundant databases with KMA","volume":"19","author":"Clausen","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"2022010507354211000_B29","doi-asserted-by":"crossref","first-page":"e80","DOI":"10.1093\/nar\/gku210","article-title":"RepARK\u2013de novo creation of repeat libraries from whole-genome NGS reads","volume":"42","author":"Koch","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2022010507354211000_B30","doi-asserted-by":"crossref","first-page":"e0150719","DOI":"10.1371\/journal.pone.0150719","article-title":"REPdenovo: inferring de novo repeat motifs from short sequence reads","volume":"11","author":"Chong","year":"2016","journal-title":"PLoS One"},{"key":"2022010507354211000_B31","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1186\/s12859-020-03779-w","article-title":"RepAHR: an improved approach for de novo repeat identification by assembly of the high-frequency reads","volume":"21","author":"Liao","year":"2020","journal-title":"BMC Bioinformatics"},{"key":"2022010507354211000_B32","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1007\/s40484-019-0166-9","article-title":"Current challenges and solutions of de novo assembly","volume":"7","author":"Liao","year":"2019","journal-title":"Quant. 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