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


RESULTS
Analysis 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.


CONCLUSIONS
T-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.
Culman
Steven W
SW
Department of Crop and Soil Sciences, Cornell University, Ithaca, NY, USA. swculman@ucdavis.edu
Bukowski
Robert
R
Gauch
Hugh G
HG
Cadillo-Quiroz
Hinsby
H
Buckley
Daniel H
DH
D000704:Analysis of Variance; D016172:DNA Fingerprinting / Q000379:methods*; D003628:Database Management Systems; D030541:Databases, Genetic; D005798:Genes, Bacterial; D020407:Internet; D015233:Models, Statistical; D012150:Polymorphism, Restriction Fragment Length; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface