A Grant

AD Kent

BK Singh

C Shyu

CA Osborne

CB Blackwood

CJ Smith

CW Kaplan

Daniel H Buckley

Hinsby Cadillo-Quiroz

Hugh G Gauch

J Dunbar

JR Cole

L Sait

R Development Core Team

RG Fitzjohn

Robert Bukowski

Steven W Culman

SW Culman

TL Marsh

Z Abdo

BMC Bioinformatics

English

PubMed

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.</p

Culman Steven W

Bukowski Robert

Gauch Hugh G

Cadillo-Quiroz Hinsby

Buckley Daniel H

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<it>T-REX</it>: software for the processing and analysis of T-RFLP data

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

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https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-10-171?site=bmcbioinformatics.biomedcentral.com

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

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