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Bioinformatics Advance Access published online on April 15, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp254
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Blaz Stres 1,*, James M. Tiedje 2 and Bostjan Murovec 3

1University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Groblje 3, 1230 Domzale, Slovenia
2Michigan State University, Department of Crop and Soil Sciences and Center for Microbial Ecology, Plant and Soil Science Building 540, MI-48828 East Lansing, USA
3 University of Ljubljana, Faculty of Electrical Engineering, Trzaska 25, 1000 Ljubljana, Slovenia

*To whom correspondence should be addressed. Dr. Blaz Stres, E-mail: blaz.stres{at}bfro.uni-lj.si


  Abstract

Summary: 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 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 labelled primer are presented.

Availability: BEsTRF is freely available at {{http://lie.fe.uni-lj.si/bestrf}} and can be downloaded from the same site.

Contact: blaz.stres{at}bfro.uni-lj.si

Supplementary information: The online protocol, numerous primer and enzyme dictionaries, sequence collections and results gener-ated during this work for various genes are available at our website {{http://lie.fe.uni-lj.si/bestrf}}.

Associate Editor: Prof. Martin Bishop

Received on February 5, 2009; revised on March 25, 2009; accepted on April 8, 2009

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