A database for ITS2 sequences from nematodes.

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  • Additional Information
    • Source:
      Publisher: BioMed Central Country of Publication: England NLM ID: 100966978 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2156 (Electronic) Linking ISSN: 14712156 NLM ISO Abbreviation: BMC Genet Subsets: MEDLINE
    • Publication Information:
      Original Publication: London : BioMed Central, [2000-
    • Subject Terms:
      Databases, Genetic*; DNA, Ribosomal Spacer/*genetics ; Nematoda/*genetics; Animals ; Computational Biology ; Genetic Markers ; Software
    • Abstract:
      Background: Marker gene surveys have a wide variety of applications in species identification, population genetics, and molecular epidemiology. As these methods expand to new types of organisms and additional markers beyond 16S and 18S rRNA genes, comprehensive databases are a critical requirement for proper analysis of these data.
      Results: Here we present an ITS2 rDNA database for marker gene surveys of both free-living and parasitic nematode populations and the software used to build the database. This is currently the most complete and up-to-date ITS2 database for nematodes and is able to reproduce previous analysis that used a smaller database.
      Conclusions: This database is an important resource for researchers working on nematodes and also provides a tool to create ITS2 databases for any given taxonomy.
    • References:
      Mol Cell Probes. 1997 Jun;11(3):201-9. (PMID: 9232619)
      Nucleic Acids Res. 2002 Jul 15;30(14):3059-66. (PMID: 12136088)
      Nat Methods. 2016 Jul;13(7):581-3. (PMID: 27214047)
      Appl Environ Microbiol. 2009 Dec;75(23):7537-41. (PMID: 19801464)
      Microbiome. 2018 Aug 9;6(1):140. (PMID: 30092815)
      Int J Parasitol. 2017 Nov;47(13):893-902. (PMID: 28797791)
      Mol Biol Evol. 2015 Nov;32(11):3030-2. (PMID: 26248563)
      PLoS One. 2015 Dec 02;10(12):e0143559. (PMID: 26630572)
      J Nematol. 1997 Dec;29(4):441-50. (PMID: 19274180)
      F1000Res. 2013 Sep 18;2:191. (PMID: 24555091)
      Bioinformatics. 2013 Nov 15;29(22):2933-5. (PMID: 24008419)
      Bioinformatics. 2012 Oct 1;28(19):2520-2. (PMID: 22908215)
      Nucleic Acids Res. 2019 Jan 8;47(D1):D259-D264. (PMID: 30371820)
      Acta Trop. 1998 Mar;69(1):1-15. (PMID: 9588237)
      Nat Methods. 2018 Jul;15(7):475-476. (PMID: 29967506)
      Nucleic Acids Res. 2018 Jan 4;46(D1):D335-D342. (PMID: 29112718)
    • Contributed Indexing:
      Keywords: Amplicon; Database; ITS2; Sequencing
    • Accession Number:
      0 (DNA, Ribosomal Spacer)
      0 (Genetic Markers)
    • Publication Date:
      Date Created: 20200712 Date Completed: 20210329 Latest Revision: 20210329
    • Publication Date:
      20221213
    • Accession Number:
      PMC7350610
    • Accession Number:
      10.1186/s12863-020-00880-0
    • Accession Number:
      32650716