{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T21:40:27Z","timestamp":1675201227610},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: BEsTRF (Best Estimated T-RF) provides a standalone environment for analyzing primers-enzymes-gene section combinations used in terminal-restriction fragment length polymorphism (T-RFLP) for its optimal resolution. User-defined sequence databases of several hundred thousand DNA sequences can be explored and the resolution of user-specified sets of primers and restriction endonucleases can be analyzed on either forward or reverse terminal fragments. Sequence quality, primer mismatches, insertions and deletions can be controlled and each primer pair-specific sequence collections can be exported for downstream analyses. The configuration for a novel T-RFLP population profiling using rpoB gene (DNA-directed RNA polymerase, beta subunit) on forward fluorescently labeled primer are presented.<\/jats:p>\n               <jats:p>Availability: BEsTRF is freely available at http:\/\/lie.fe.uni-lj.si\/bestrf and can be downloaded from the same site. The online protocol, numerous primer and enzyme dictionaries, sequence collections and results generated during this work for various genes are available at our website http:\/\/lie.fe.uni-lj.si\/bestrf.<\/jats:p>\n               <jats:p>Contact: \u00a0blaz.stres@bfro.uni-lj.si<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp254","type":"journal-article","created":{"date-parts":[[2009,4,16]],"date-time":"2009-04-16T01:28:58Z","timestamp":1239845338000},"page":"1556-1558","source":"Crossref","is-referenced-by-count":9,"title":["BEsTRF: a tool for optimal resolution of terminal-restriction fragment length polymorphism analysis based on user-defined primer\u2013enzyme\u2013sequence databases"],"prefix":"10.1093","volume":"25","author":[{"given":"Bla\u017e","family":"Stres","sequence":"first","affiliation":[{"name":"1 Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Dom\u017eale, Slovenia, 2Department of Crop and Soil Sciences, and Center for Microbial Ecology, Plant and Soil Science, Michigan State University, Building 540, MI-48828 East Lansing, USA and 3Faculty of Electrical Engineering, University of Ljubljana, Tr\u017ea\u0161ka 25, 1000 Ljubljana, Slovenia"}]},{"given":"James M.","family":"Tiedje","sequence":"additional","affiliation":[{"name":"1 Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Dom\u017eale, Slovenia, 2Department of Crop and Soil Sciences, and Center for Microbial Ecology, Plant and Soil Science, Michigan State University, Building 540, MI-48828 East Lansing, USA and 3Faculty of Electrical Engineering, University of Ljubljana, Tr\u017ea\u0161ka 25, 1000 Ljubljana, Slovenia"}]},{"given":"Bo\u0161tjan","family":"Murovec","sequence":"additional","affiliation":[{"name":"1 Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Dom\u017eale, Slovenia, 2Department of Crop and Soil Sciences, and Center for Microbial Ecology, Plant and Soil Science, Michigan State University, Building 540, MI-48828 East Lansing, USA and 3Faculty of Electrical Engineering, University of Ljubljana, Tr\u017ea\u0161ka 25, 1000 Ljubljana, Slovenia"}]}],"member":"286","published-online":{"date-parts":[[2009,4,15]]},"reference":[{"key":"2023013112012657500_B1","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1128\/aem.62.3.872-879.1996","article-title":"A computer analysis of primer and probe hybridization potential with bacterial small-subunit rRNA sequences","volume":"62","author":"Brunk","year":"1996","journal-title":"Appl. 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