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

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http://pubman.mpdl.mpg.de/cone/persons/resource/persons61277

Junier,  Pilar
Department Ecophysiology, Max Planck Institute for Limnology, Max Planck Institute for Evolutionary Biology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons57008

Witzel,  Karl-Paul
Department Ecophysiology, Max Planck Institute for Limnology, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Citation

Junier, P., Junier, T., & Witzel, K.-P. (2008). TRiFLe, a program for in silico terminal restriction fragment length polymorphism analysis with user-defined sequence sets. Applied and Environmental Microbiology, 74(20), 6452-6456. doi:10.1128/AEM.01394-08.


Cite as: http://hdl.handle.net/11858/00-001M-0000-000F-D65D-2
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.