ArticleBioinformatics (Oxford, England)2018
Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed, 47 citations in OpenAlex.
- Genetic sequencing of the airborne fungal spectrum and air quality at a public hospital in Mexico City.PLOS global public health · 2025Article
- Diversity and Composition of the Airborne Fungal Community in Mexico City with a Metagenomic Approach.Microorganisms · 2024Article
- Impact of florfenicol dosing regimen on the phenotypic and genotypic resistance of enteric bacteria in steers.Scientific reports · 2024Article
- Article
- An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics.Microbiome · 2022Article
- Central role of intestinal epithelial glucocorticoid receptor in alcohol- and corticosterone-induced gut permeability and systemic response.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2022Article
- Chronic stress and corticosterone exacerbate alcohol-induced tissue injury in the gut-liver-brain axis.Scientific reports · 2021Article
- Longitudinal Metatranscriptomic Analysis of a Meat Spoilage Microbiome Detects Abundant Continued Fermentation and Environmental Stress Responses during Shelf Life and Beyond.Applied and environmental microbiology · 2020Article
- Improving bee health through genomics.Nature reviews. Genetics · 2020Review
- The effect of antibiotics on the gut microbiome: a metagenomics analysis of microbial shift and gut antibiotic resistance in antibiotic treated mice.BMC genomics · 2020Article
- Article
- DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products.BMC genomics · 2019Article
- Article
- Over 2.5 million COI sequences in GenBank and growing.PloS one · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 10 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data. Results: We evaluated the Metaxa2 Database Builder on 11 commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality. Availability and implementation: Freely available on the web as part of the Metaxa2 package at http://microbiology.se/software/metaxa2/. Supplementary information: Supplementary data are available at Bioinformatics online.
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.