Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI

Average nucleotide identity analysis is a useful tool to verify taxonomic identities in prokaryotic genomes, for both complete and draft assemblies. Using optimum threshold ranges appropriate for different prokaryotic taxa, we have reviewed all prokaryotic genome assemblies in GenBank with regard to...

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Autores principales: Ciufo, Stacy, Kannan, Sivakumar, Sharma, Shobha, Badretdin, Azat, Clark, Karen, Turner, Seán, Brover, Slava, Schoch, Conrad L., Kimchi, Avi, DiCuccio, Michael
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2018
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6978984/
https://www.ncbi.nlm.nih.gov/pubmed/29792589
http://dx.doi.org/10.1099/ijsem.0.002809
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author Ciufo, Stacy
Kannan, Sivakumar
Sharma, Shobha
Badretdin, Azat
Clark, Karen
Turner, Seán
Brover, Slava
Schoch, Conrad L.
Kimchi, Avi
DiCuccio, Michael
author_facet Ciufo, Stacy
Kannan, Sivakumar
Sharma, Shobha
Badretdin, Azat
Clark, Karen
Turner, Seán
Brover, Slava
Schoch, Conrad L.
Kimchi, Avi
DiCuccio, Michael
author_sort Ciufo, Stacy
collection PubMed
description Average nucleotide identity analysis is a useful tool to verify taxonomic identities in prokaryotic genomes, for both complete and draft assemblies. Using optimum threshold ranges appropriate for different prokaryotic taxa, we have reviewed all prokaryotic genome assemblies in GenBank with regard to their taxonomic identity. We present the methods used to make such comparisons, the current status of GenBank verifications, and recent developments in confirming species assignments in new genome submissions.
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spelling pubmed-69789842020-01-27 Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI Ciufo, Stacy Kannan, Sivakumar Sharma, Shobha Badretdin, Azat Clark, Karen Turner, Seán Brover, Slava Schoch, Conrad L. Kimchi, Avi DiCuccio, Michael Int J Syst Evol Microbiol Research Article Average nucleotide identity analysis is a useful tool to verify taxonomic identities in prokaryotic genomes, for both complete and draft assemblies. Using optimum threshold ranges appropriate for different prokaryotic taxa, we have reviewed all prokaryotic genome assemblies in GenBank with regard to their taxonomic identity. We present the methods used to make such comparisons, the current status of GenBank verifications, and recent developments in confirming species assignments in new genome submissions. Microbiology Society 2018-07 2018-05-24 /pmc/articles/PMC6978984/ /pubmed/29792589 http://dx.doi.org/10.1099/ijsem.0.002809 Text en © 2018 IUMS http://creativecommons.org/licenses/by/4.0/ This is an open access article under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Ciufo, Stacy
Kannan, Sivakumar
Sharma, Shobha
Badretdin, Azat
Clark, Karen
Turner, Seán
Brover, Slava
Schoch, Conrad L.
Kimchi, Avi
DiCuccio, Michael
Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI
title Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI
title_full Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI
title_fullStr Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI
title_full_unstemmed Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI
title_short Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI
title_sort using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the ncbi
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6978984/
https://www.ncbi.nlm.nih.gov/pubmed/29792589
http://dx.doi.org/10.1099/ijsem.0.002809
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