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Applied and Environmental Microbiology, October 2008, p. 6452-6456, Vol. 74, No. 20
0099-2240/08/$08.00+0     doi:10.1128/AEM.01394-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

TRiFLe, a Program for In Silico Terminal Restriction Fragment Length Polymorphism Analysis with User-Defined Sequence Sets {triangledown}

Pilar Junier,1,3*,{dagger} Thomas Junier,2,{dagger} and Karl-Paul Witzel3

Environmental Microbiology Laboratory, Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne, Switzerland,1 Computational Evolutionary Genomics Group, University of Geneva, CH-1211 Geneva, Switzerland,2 Max Planck Institute for Evolutionary Biology, 24306 Ploen, Germany3

Received 21 June 2008/ Accepted 19 August 2008

We describe TRiFLe, a freely accessible computer program that generates theoretical terminal restriction fragments (T-RFs) from any user-supplied sequence set tailored to a particular group of organisms, sequences from clone libraries, or sequences from specific genes. The program allows a rapid identification of the most polymorphic enzymes, creates a collection of T-RFs for the data set, and can potentially identify specific T-RFs in T-RF length polymorphism (T-RFLP) patterns by comparing theoretical and experimental results. TRiFLE was used for analyzing T-RFLP data generated for the amoA and pmoA genes. The peaks identified in the T-RFLP patterns show an overlap of ammonia- and methane-oxidizing bacteria in the metalimnion of a subtropical lake.

* Corresponding author. Mailing address: EPFL ENAC ISTE EML, CE 1 644 (Centre Est), Station 6, CH-1015 Lausanne, Switzerland. Phone: 41 21 693 63 96. Fax: 41 21 693 62 05. E-mail: pilar.junier{at}epfl.ch

{triangledown} Published ahead of print on 29 August 2008.

{dagger} These authors contributed equally to the manuscript.

Applied and Environmental Microbiology, October 2008, p. 6452-6456, Vol. 74, No. 20
0099-2240/08/$08.00+0     doi:10.1128/AEM.01394-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.





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