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Scientific article
English

TRiFLe, a program for in silico terminal restriction fragment length polymorphism analysis with user-defined sequence sets

Published inApplied and environmental microbiology, vol. 74, no. 20, p. 6452-6456
Publication date2008
Abstract

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.

Keywords
  • Bacteria/genetics
  • Computational Biology/*methods
  • DNA Fingerprinting/*methods
  • *Polymorphism, Restriction Fragment Length
Citation (ISO format)
JUNIER, Pilar, JUNIER, Thomas, WITZEL, Karl-Paul. TRiFLe, a program for in silico terminal restriction fragment length polymorphism analysis with user-defined sequence sets. In: Applied and environmental microbiology, 2008, vol. 74, n° 20, p. 6452–6456. doi: 10.1128/AEM.01394-08
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ISSN of the journal0099-2240
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