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Title

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

Authors
Junier, Pilar
Witzel, Karl-Paul
Published in Applied and Environmental Microbiology. 2008, vol. 74, no. 20, p. 6452-6456
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/geneticsComputational Biology/*methodsDNA Fingerprinting/*methods*Polymorphism, Restriction Fragment Length
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PMID: 18757578
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Other version: http://aem.asm.org/content/74/20/6452.full.pdf
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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. https://archive-ouverte.unige.ch/unige:19046

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Deposited on : 2012-03-27

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