TRiFLe, a program for in silico terminal restriction fragment length polymorphism analysis with user-defined sequence sets.
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.
Junier
Pilar
P
Environmental Microbiology Laboratory, Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne, Switzerland. pilar.junier@epfl.ch
Junier
Thomas
T
Witzel
Karl-Paul
KP