ArticleNucleic acids research2011
ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 218 papers.
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Who cites it
218 citing papers in PubMed.
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- Impact of Rainfall on Aquatic and Terrestrial Species Monitoring Using Riverine Environmental DNA.Ecology and evolution · 2026Article
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- Urbanization Drives Patterns of Individual Specialization but Not Dietary Diversity Among Coyotes.Ecology and evolution · 2026Article
- Using Metabarcoding Techniques to Map Multiple Dung Beetle-Vertebrate iDNA Networks in a Southeast Asian Forest.Molecular ecology resources · 2026Article
- Individual Identification of Prey in Carnivore Scats.Molecular ecology resources · 2026Article
- Operationalising Environmental DNA (eDNA) Detection of Major Malaria Vector Species in Ghana.Molecular ecology resources · 2026Article
- Real-time genomic pathogen, resistance, and host range characterization from passive water sampling of wetland ecosystems.Applied and environmental microbiology · 2026Article
- Evaluating the Molecular Potential and Interpretability of DNA in Historical Spirit Collection Media.Molecular ecology resources · 2026Article
- DIY: A Practical Field-to-Sequencer Workflow for Metabarcoding the Diet of Terrestrial Carnivore Species.Molecular ecology resources · 2026Article
- A multi-modal dataset for insect biodiversity with imagery and DNA at the trap and individual level.Scientific data · 2026Article
- A Breath of Fresh Air: A Novel Passive Airborne eDNA Approach for Scalable Terrestrial Biodiversity Monitoring.Ecology and evolution · 2026Article
- Diet and Prey Preference of Tigers (Ecology and evolution · 2026Article
- Article
- Environmental DNA metabarcoding facilitates integrative conservation assessments and species rediscoveries in tropical biodiversity hotspots.Scientific reports · 2026Article
- MitoNGS: an online platform to analyze fish metabarcoding data in high resolution.Molecular biology and evolution · 2026Article
158 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Using non-conventional markers, DNA metabarcoding allows biodiversity assessment from complex substrates. In this article, we present ecoPrimers, a software for identifying new barcode markers and their associated PCR primers. ecoPrimers scans whole genomes to find such markers without a priori knowledge. ecoPrimers optimizes two quality indices measuring taxonomical range and discrimination to select the most efficient markers from a set of reference sequences, according to specific experimental constraints such as marker length or specifically targeted taxa. The key step of the algorithm is the identification of conserved regions among reference sequences for anchoring primers. We propose an efficient algorithm based on data mining, that allows the analysis of huge sets of sequences. We evaluate the efficiency of ecoPrimers by running it on three different sequence sets: mitochondrial, chloroplast and bacterial genomes. Identified barcode markers correspond either to barcode regions already in use for plants or animals, or to new potential barcodes. Results from empirical experiments carried out on a promising new barcode for analyzing vertebrate diversity fully agree with expectations based on bioinformatics analysis. These tests demonstrate the efficiency of ecoPrimers for inferring new barcodes fitting with diverse experimental contexts. ecoPrimers is available as an open source project at: http://www.grenoble.prabi.fr/trac/ecoPrimers.
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