Matthew L Workentine, Rebecca Chen, Shawna Zhu, Stefan Gavriliuc, Nicolette Shaw, Jill de Rijke, Elizabeth M Redman, Russell W Avramenko, Janneke Wit, Jocelyn Poissant, John S Gilleard
{"title":"线虫ITS2序列数据库。","authors":"Matthew L Workentine, Rebecca Chen, Shawna Zhu, Stefan Gavriliuc, Nicolette Shaw, Jill de Rijke, Elizabeth M Redman, Russell W Avramenko, Janneke Wit, Jocelyn Poissant, John S Gilleard","doi":"10.1186/s12863-020-00880-0","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Marker gene surveys have a wide variety of applications in species identification, population genetics, and molecular epidemiology. As these methods expand to new types of organisms and additional markers beyond 16S and 18S rRNA genes, comprehensive databases are a critical requirement for proper analysis of these data.</p><p><strong>Results: </strong>Here we present an ITS2 rDNA database for marker gene surveys of both free-living and parasitic nematode populations and the software used to build the database. This is currently the most complete and up-to-date ITS2 database for nematodes and is able to reproduce previous analysis that used a smaller database.</p><p><strong>Conclusions: </strong>This database is an important resource for researchers working on nematodes and also provides a tool to create ITS2 databases for any given taxonomy.</p>","PeriodicalId":9197,"journal":{"name":"BMC Genetics","volume":" ","pages":"74"},"PeriodicalIF":2.9000,"publicationDate":"2020-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12863-020-00880-0","citationCount":"28","resultStr":"{\"title\":\"A database for ITS2 sequences from nematodes.\",\"authors\":\"Matthew L Workentine, Rebecca Chen, Shawna Zhu, Stefan Gavriliuc, Nicolette Shaw, Jill de Rijke, Elizabeth M Redman, Russell W Avramenko, Janneke Wit, Jocelyn Poissant, John S Gilleard\",\"doi\":\"10.1186/s12863-020-00880-0\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Marker gene surveys have a wide variety of applications in species identification, population genetics, and molecular epidemiology. As these methods expand to new types of organisms and additional markers beyond 16S and 18S rRNA genes, comprehensive databases are a critical requirement for proper analysis of these data.</p><p><strong>Results: </strong>Here we present an ITS2 rDNA database for marker gene surveys of both free-living and parasitic nematode populations and the software used to build the database. This is currently the most complete and up-to-date ITS2 database for nematodes and is able to reproduce previous analysis that used a smaller database.</p><p><strong>Conclusions: </strong>This database is an important resource for researchers working on nematodes and also provides a tool to create ITS2 databases for any given taxonomy.</p>\",\"PeriodicalId\":9197,\"journal\":{\"name\":\"BMC Genetics\",\"volume\":\" \",\"pages\":\"74\"},\"PeriodicalIF\":2.9000,\"publicationDate\":\"2020-07-10\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://sci-hub-pdf.com/10.1186/s12863-020-00880-0\",\"citationCount\":\"28\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"BMC Genetics\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1186/s12863-020-00880-0\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"Biochemistry, Genetics and Molecular Biology\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"BMC Genetics","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1186/s12863-020-00880-0","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}
Background: Marker gene surveys have a wide variety of applications in species identification, population genetics, and molecular epidemiology. As these methods expand to new types of organisms and additional markers beyond 16S and 18S rRNA genes, comprehensive databases are a critical requirement for proper analysis of these data.
Results: Here we present an ITS2 rDNA database for marker gene surveys of both free-living and parasitic nematode populations and the software used to build the database. This is currently the most complete and up-to-date ITS2 database for nematodes and is able to reproduce previous analysis that used a smaller database.
Conclusions: This database is an important resource for researchers working on nematodes and also provides a tool to create ITS2 databases for any given taxonomy.
期刊介绍：
BMC Genetics is an open access, peer-reviewed journal that considers articles on all aspects of inheritance and variation in individuals and among populations.
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