BEsTRF

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

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

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.

Keywords

mikrobiologija;molekularna genetika;BEsTRF;

Data

Language:	English
Year of publishing:	2009
Typology:	1.01 - Original Scientific Article
Organization:	UL BF - Biotechnical Faculty
UDC:	579:575
COBISS:	2450312
ISSN:	1367-4803
Views:	1286
Downloads:	437
Average score:	0 (0 votes)
Metadata:

Other data

Secondary language:	Unknown
Type (COBISS):	Not categorized
Pages:	str. 1556-1558
Volume:	ǂIssue ǂ12
Issue:	ǂVol. ǂ25
Chronology:	2009
DOI:	10.1093/bioinformatics/btp254
ID:	21392