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Bioinformatics Advance Access originally published online on April 15, 2009
Bioinformatics 2009 25(12):1556-1558; 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 analysis based on user-defined primer–enzyme–sequence databases

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

1Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Domzale, 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, Trzaska 25, 1000 Ljubljana, Slovenia

*To whom correspondence should be addressed.


  Abstract

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.

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.

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

Associate Editor: Martin Bishop

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

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