BEsTRF : a tool for optimal resolution of terminal-restriction fragment length polymorphism (T-RFLP) analysis based on user defined primer-enzyme-sequence databases

Stres, Blaž (author), Tiedje, James M. (author), Murovec, Boštjan (author)

BEsTRF (Best Estimated T-RF) provides a stand-alone environment for analyzing primers-enzymes-gene section combinations used in 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 delitions 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 labelled primer are presented.

• Language: English
• Keywords: mikrobiologija, molekularna genetika, BEsTRF
• Work type: Not categorized
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Year: 2009
• Number of pages: Str. 1556-1558
• Numbering: Vol. 25, Issue 12
• PID: 20.500.12556/RUL-32827
• UDC: 579:575
• ISSN on article: 1367-4803
• DOI: 10.1093/bioinformatics/btp254
• COBISS.SI-ID: 2450312
• Publication date in RUL: 10.07.2015