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

Steven W. Culman, Robert Bukowski, Hugh G. Gauch, Hinsby Cadillo-Quiroz, Daniel H. Buckley

Research output: Contribution to journalArticle

317 Citations (Scopus)

Abstract

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. Conclusion: 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.

Original languageEnglish (US)
Article number171
JournalBMC Bioinformatics
Volume10
DOIs
StatePublished - Jun 6 2009
Externally publishedYes

Fingerprint

Polymorphism
Restriction Fragment Length Polymorphisms
Fragment
Software
Restriction
Processing
Bins
Main Effect
Design of experiments
Noise
Labels
Research Design
Fingerprinting
Interaction Effects
Research
Factorial
Experimental design
Baseline
Multiplicative
Attribute

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Structural Biology
  • Applied Mathematics

Cite this

T-REX : Software for the processing and analysis of T-RFLP data. / Culman, Steven W.; Bukowski, Robert; Gauch, Hugh G.; Cadillo-Quiroz, Hinsby; Buckley, Daniel H.

In: BMC Bioinformatics, Vol. 10, 171, 06.06.2009.

Research output: Contribution to journalArticle

Culman, Steven W. ; Bukowski, Robert ; Gauch, Hugh G. ; Cadillo-Quiroz, Hinsby ; Buckley, Daniel H. / T-REX : Software for the processing and analysis of T-RFLP data. In: BMC Bioinformatics. 2009 ; Vol. 10.
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