T-REX: software for the processing and analysis of T-RFLP data

By Steven W. Culman, R. Bukowski, Hugh G. Jr Gauch, H. Cadillo-Quiroz, D. Buckley. BMC Bioinformatics, 2009

460 citations recorded by the source corpus.

BackgroundDespite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) and other microbial community fingerprinting techniques, there are still numerous obstacles that hamper the analysis of these datasets. Many steps are required to process raw data into a format ready for analysis and interpretation. These steps can be time-intensive, error-prone, and can introduce unwanted variability into the analysis. Accordingly, we developed T-REX, free, online software for the processing and analysis of T-RFLP data.ResultsAnalysis of T-RFLP data generated from a multiple-factorial study was performed with T-REX. With this software, we were able to i) label raw data with attributes related to the experimental design of the samples, ii) determine a baseline threshold for identification of true peaks over noise, iii) align terminal restriction fragments (T-RFs) in all samples (i.e., bin T-RFs), iv) construct a two-way data matrix from labeled data and process the matrix in a variety of ways, v) produce several measures of data matrix complexity, including the distribution of variance between main and interaction effects and sample heterogeneity, and vi) analyze a data matrix with the additive main effects and multiplicative interaction (AMMI) model.ConclusionT-REX provides a free, platform-independent tool to the research community that allows for an integrated, rapid, and more robust analysis of T-RFLP data.

Subfields: Ecology, Health, Toxicology and Mutagenesis, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3289175b8631b36ba63c43770e13061362b73eb1

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

In Molecular Biology

Citations in the corpus

Total and active microbial communities and phoD as affected by phosphate depletion and pH in soil (2016, methodology): “T-RFLP profiles were processed and analyzed with the T-REX program (Culman et al. 2009), using the peak area to identify operational taxonomic units (OTUs) and a clustering threshold of 0.5 bp. Analysis of total and active phoD-harboring community structure and composition using 454-sequencing The…”
Relative importance of soil properties and microbial community for soil functionality: insights from a microbial swap experiment (2016, methodology): “After ensuring that the quality of the capillary electrophoresis run was satisfactory, relative abundance tables were obtained for statistical analysis from GeneMapper and T-rex (Culman et al. 2009).”
Soil microbial diversity and activity linked to crop yield and quality in a dryland organic wheat production system (2016, methodology): “The peak area standard deviation multiplier used in this case was 1 (the standard T-REX default).”