ArticleBMC bioinformatics2009
T-REX: software for the processing and analysis of T-RFLP data.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
104 citing papers in PubMed.
- Urinary catheter-associated microbiota change in accordance with treatment and infection status.PloS one · 2017Trial
- A Nitrate-Transforming Bacterial Community Dominates in theMicroorganisms · 2023Article
- Phosphate fertilization affects rhizosphere microbiome of maize and sorghum genotypes.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2022Article
- Salivary Microbiota Is Significantly Less Diverse in Patients with Chronic Spontaneous Urticaria Compared to Healthy Controls: Preliminary Results.Life (Basel, Switzerland) · 2021Article
- Broad diversity of bacteria degrading 17ß-estradiol-3-sulfate isolated from river sediment and biofilm at a wastewater treatment plant discharge.Archives of microbiology · 2021Article
- Environmental parameters and microbial community profiles as indication towards microbial activities and diversity in aquaponic system compartments.BMC microbiology · 2021Article
- Inoculation of grape musts with single strains of Saccharomyces cerevisiae yeast reduces the diversity of chemical profiles of wines.PloS one · 2021Article
- Season of Birth Impacts the Neonatal Nasopharyngeal Microbiota.Children (Basel, Switzerland) · 2020Article
- Preparation and characterization of site-specific dechlorinating microbial inocula capable of complete dechlorination enriched in anaerobic microcosms amended with clay mineral.World journal of microbiology & biotechnology · 2020Article
- Article
- Cryopreservation and Resuscitation of Natural Aquatic Prokaryotic Communities.Frontiers in microbiology · 2020Article
- Plant-driven niche differentiation of ammonia-oxidizing bacteria and archaea in global drylands.The ISME journal · 2019Article
- Vulnerability of Soil Microbiome to Monocropping of Medicinal and Aromatic Plants and Its Restoration Through Intercropping and Organic Amendments.Frontiers in microbiology · 2019Article
- Article
- Rapid Microbial Dynamics in Response to an Induced Wetting Event in Antarctic Dry Valley Soils.Frontiers in microbiology · 2019Article
- Herbivore removal reduces influence of arbuscular mycorrhizal fungi on plant growth and tolerance in an East African savanna.Oecologia · 2018Article
- A comparison study of the potential risks induced in arable land and forest soils by carcass-derived pollutants.Environmental geochemistry and health · 2018Article
- Responses of an Agricultural Soil Microbiome to Flooding with Seawater after Managed Coastal Realignment.Microorganisms · 2018Article
- Toward Integrative Bacterial Monitoring of Metolachlor Toxicity in Groundwater.Frontiers in microbiology · 2018Article
- Article
44 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.