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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)

URLURL - Presentation file, Visit http://bioinformatics.oxfordjournals.org/cgi/reprint/btp254?ijkey=qw9y7y9LEcKhXd7&keytype=ref New window

Abstract
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 (r6)
Tipology:1.01 - Original Scientific Article
Organization:BF - Biotechnical Faculty
Year:2009
Number of pages:str. 1556-1558
Numbering:Vol. 25, Issue 12
UDC:579:575
ISSN on article:1367-4803
DOI:10.1093/bioinformatics/btp254 Link is opened in a new window
COBISS.SI-ID:2450312 Link is opened in a new window
Views:580
Downloads:317
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