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Pest Alert Tool-a web-based application for flagging species of concern in metabarcoding datasets.

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  • معلومة اضافية
    • المصدر:
      Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
    • بيانات النشر:
      Publication: 1992- : Oxford : Oxford University Press
      Original Publication: London, Information Retrieval ltd.
    • الموضوع:
      DNA Barcoding, Taxonomic* ; Ecosystem* ; DNA, Environmental*/analysis ; Introduced Species*; Biodiversity ; Internet ; Phylogeny ; High-Throughput Screening Assays ; Mobile Applications
    • نبذة مختصرة :
      Advances in high-throughput sequencing (HTS) technologies and their increasing affordability have fueled environmental DNA (eDNA) metabarcoding data generation from freshwater, marine and terrestrial ecosystems. Research institutions worldwide progressively employ HTS for biodiversity assessments, new species discovery and ecological trend monitoring. Moreover, even non-scientists can now collect an eDNA sample, send it to a specialized laboratory for analysis and receive in-depth biodiversity record from a sampling site. This offers unprecedented opportunities for biodiversity assessments across wide temporal and spatial scales. The large volume of data produced by metabarcoding also enables incidental detection of species of concern, including non-indigenous and pathogenic organisms. We introduce an online app-Pest Alert Tool-for screening nuclear small subunit 18S ribosomal RNA and mitochondrial cytochrome oxidase subunit I datasets for marine non-indigenous species as well as unwanted and notifiable marine organisms in New Zealand. The output can be filtered by minimum length of the query sequence and identity match. For putative matches, a phylogenetic tree can be generated through the National Center for Biotechnology Information's BLAST Tree View tool, allowing for additional verification of the species of concern detection. The Pest Alert Tool is publicly available at https://pest-alert-tool-prod.azurewebsites.net/.
      (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)
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    • الرقم المعرف:
      0 (DNA, Environmental)
    • الموضوع:
      Date Created: 20230519 Date Completed: 20230712 Latest Revision: 20230718
    • الموضوع:
      20231215
    • الرقم المعرف:
      PMC10320087
    • الرقم المعرف:
      10.1093/nar/gkad364
    • الرقم المعرف:
      37207328