Molecular Acquisition, Cleaning and Evaluation in R (MACER) - A tool to assemble molecular marker datasets from BOLD and GenBank

Young, Reginald H.F.; Gill, Rekkab; Gillis, Daniel; Hanner, Robert

doi:10.3897/bdj.9.e71378

Cited by 5 publications

(3 citation statements)

References 30 publications

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“…Similar computational and statistical tools, in the form of MATLAB packages, R packages, Python packages and methodological pipelines, used to assess anomalies in DNA (meta)barcodes, have been released. Examples include divisive hierarchical clustering: DADA ( Rosen et al 2012 ) and DADA2 ( Callahan et al 2016 ); artificial neural networks: ( Ma et al 2018 ); Profile Hidden Markov Models: coil ( Nugent et al 2020 ), debar ( Nugent et al 2021 and Porter and Hajibabaei 2021 ); distribution sample quantiles: MACER ( Young et al 2021 ); and Shannon entropy: SequenceBouncer ( Dunn 2021 ), A2G2 ( Hleap et al 2020 ), DnoisE ( Antich et al 2022 and Turon et al 2020 ). These methods and programmes are beginning to see widespread use within the biodiversity and regulatory science communities.…”

Section: Discussionmentioning

confidence: 99%

VLF: An R package for the analysis of very low frequency variants in DNA sequences

Phillips¹,

Athey²,

McNicholas³

et al. 2023

BDJ

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Here, we introduce VLF, an R package to determine the distribution of very low frequency variants (VLFs) in nucleotide and amino acid sequences for the analysis of errors in DNA sequence records. The package allows users to assess VLFs in aligned and trimmed protein-coding sequences by automatically calculating the frequency of nucleotides or amino acids in each sequence position and outputting those that occur under a user-specified frequency (default of p = 0.001). These results can then be used to explore fundamental population genetic and phylogeographic patterns, mechanisms and processes at the microevolutionary level, such as nucleotide and amino acid sequence conservation. Our package extends earlier work pertaining to an implementation of VLF analysis in Microsoft Excel, which was found to be both computationally slow and error prone. We compare those results to our own herein. Results between the two implementations are found to be highly consistent for a large DNA barcode dataset of bird species. Differences in results are readily explained by both manual human error and inadequate Linnean taxonomy (specifically, species synonymy). Here, VLF is also applied to a subset of avian barcodes to assess the extent of biological artifacts at the species level for Canada goose (Branta canadensis), as well as within a large dataset of DNA barcodes for fishes of forensic and regulatory importance. The novelty of VLF and its benefit over the previous implementation include its high level of automation, speed, scalability and ease-of-use, each desirable characteristics which will be extremely valuable as more sequence data are rapidly accumulated in popular reference databases, such as BOLD and GenBank.

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Section: Discussionmentioning

confidence: 99%

VLF: An R package for the analysis of very low frequency variants in DNA sequences

Phillips¹,

Athey²,

McNicholas³

et al. 2023

BDJ

Self Cite

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“…DNA sequences were obtained for selected taxa from NCBI GenBank and the Barcode of Life Datasystems with the R (R Core Team, 2020) package MACER (V 2.1) (Young et al, 2021) using the auto_seq_download() function with default settings. A total of 19 species of tuna and common substitutes were included in this study as outlined in Table 3.…”

Section: Inclusion/exclusion Criteriamentioning

confidence: 99%

Twenty‐three years of PCR‐based seafood authentication assay development: What have we learned?

Singh,

Young,

Hellberg

et al. 2024

Comp Rev Food Sci Food Safe

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Seafood is a prime target for fraudulent activities due to the complexity of its supply chain, high demand, and difficult discrimination among species once morphological characteristics are removed. Instances of seafood fraud are expected to increase due to growing demand. This manuscript reviews the application of DNA‐based methods for commercial fish authentication and identification from 2000 to 2023. It explores (1) the most common types of commercial fish used in assay development, (2) the type of method used, (3) the gene region most often targeted, (4) provides a case study of currently published assays or primer‐probe pairs used for DNA amplification, for specificity, and (5) makes recommendations for ensuring standardized assay‐based reporting for future studies. A total of 313 original assays for the detection and authentication of commercial fish species from 191 primary articles published over the last 23 years were examined. The most explored DNA‐based method was real‐time polymerase chain reaction (qPCR), followed by DNA sequencing. The most targeted gene regions were cytb (cytochrome b) and COI (cytochrome c oxidase 1). Tuna was the most targeted commercial fish species. A case study of published tuna assays (n = 19) targeting the cytb region found that most assays were not species‐specific through in silico testing. This was conducted by examining the primer mismatch for each assay using multiple sequence alignment. Therefore, there is need for more standardized DNA‐based assay reporting in the literature to ensure specificity, reproducibility, and reliability of results. Factors, such as cost, sensitivity, quality of the DNA, and species, should be considered when designing assays.

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“…In addition, many computational resources and software have been developed to accommodate the expanding role of DNA barcodes. Some of these packages (e.g., MDOP [19]) help researchers to organize DNA barcoding data before uploading to databases, such as BOLD and NCBI's Genbank, and still others are designed to assess the quality of data that have already been made publicly available (e.g., BAGS [20] and MACER [21]). The quality of DNA barcode data can be impacted by a number of factors, including poor sequence annotation, a lack of physical specimen vouchers, poor sequence quality, and incorrect consensus sequence building.…”

Section: Novel Computational Resources and Softwarementioning

confidence: 99%

The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

Gostel

Kress

2022

Diversity

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DNA barcoding has transformed the fields of ecology, evolution, and conservation by providing a rapid and effective tool for species identification. The growth of DNA barcodes as a resource for biologists has followed advances in computational and sequencing technology that have enabled high-throughput barcoding applications. The global DNA barcode database is expanding to represent the diversity of species on Earth thanks to efforts by international consortia and expanding biological collections. Today, DNA barcoding is instrumental in advancing our understanding of how species evolve, how they interact, and how we can slow down their extirpation and extinction. This review focuses on current applications of DNA barcode sequences to address fundamental lines of research, as well as new and expanding applications of which DNA barcoding will play a central role.

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Molecular Acquisition, Cleaning and Evaluation in R (MACER) - A tool to assemble molecular marker datasets from BOLD and GenBank

Cited by 5 publications

References 30 publications

VLF: An R package for the analysis of very low frequency variants in DNA sequences

VLF: An R package for the analysis of very low frequency variants in DNA sequences

Twenty‐three years of PCR‐based seafood authentication assay development: What have we learned?

The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

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