TRiFLe, a program for in silico terminal restriction fragment length polymorphism analysis with user-defined sequence sets
TRiFLe, a program for in silico terminal restriction fragment length polymorphism analysis with user-defined sequence sets
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DOI：
10.1128/aem.01394-08
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发表时间：
2008-10-01
影响因子：
4.4
通讯作者：
Witzel, Karl-Paul
中科院分区：
文献类型：
--
作者：
Junier, Pilar;Junier, Thomas;Witzel, Karl-Paul
我们描述TRiFLe，一个免费访问的计算机程序，生成理论的末端限制性片段（T-RFs）从任何用户提供的序列集定制的一个特定的生物体，克隆库的序列，或特定基因的序列。该程序允许快速识别最多态性的酶，创建一个集合的T-RF的数据集，并可以潜在地识别特定的T-RF的T-RF长度多态性（T-RFLP）模式通过比较理论和实验结果。TRiFLE用于分析针对amoA和pmoA基因生成的T-RFLP数据。在T-RFLP模式中确定的峰显示重叠的氨和甲烷氧化细菌在亚热带湖泊的metalimonion。
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.