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ANItools web: a web tool for fast genome comparison within multiple bacterial strains

Background: Early classification of prokaryotes was based solely on phenotypic similarities, but modern prokaryote characterization has been strongly influenced by advances in genetic methods. With the fast development of the sequencing technology, the ever increasing number of genomic sequences per...

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Detalles Bibliográficos
Autores principales: Han, Na, Qiang, Yujun, Zhang, Wen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911789/
https://www.ncbi.nlm.nih.gov/pubmed/27270714
http://dx.doi.org/10.1093/database/baw084
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author Han, Na
Qiang, Yujun
Zhang, Wen
author_facet Han, Na
Qiang, Yujun
Zhang, Wen
author_sort Han, Na
collection PubMed
description Background: Early classification of prokaryotes was based solely on phenotypic similarities, but modern prokaryote characterization has been strongly influenced by advances in genetic methods. With the fast development of the sequencing technology, the ever increasing number of genomic sequences per species offers the possibility for developing distance determinations based on whole-genome information. The average nucleotide identity (ANI), calculated from pair-wise comparisons of all sequences shared between two given strains, has been proposed as the new metrics for bacterial species definition and classification. Results: In this study, we developed the web version of ANItools (http://ani.mypathogen.cn/), which helps users directly get ANI values from online sources. A database covering ANI values of any two strains in a genus was also included (2773 strains, 1487 species and 668 genera). Importantly, ANItools web can automatically run genome comparison between the input genomic sequence and data sequences (Genus and Species levels), and generate a graphical report for ANI calculation results. Conclusion: ANItools web is useful for defining the relationship between bacterial strains, further contributing to the classification and identification of bacterial species using genome data. Database URL: http://ani.mypathogen.cn/
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spelling pubmed-49117892016-06-20 ANItools web: a web tool for fast genome comparison within multiple bacterial strains Han, Na Qiang, Yujun Zhang, Wen Database (Oxford) Database Tool Background: Early classification of prokaryotes was based solely on phenotypic similarities, but modern prokaryote characterization has been strongly influenced by advances in genetic methods. With the fast development of the sequencing technology, the ever increasing number of genomic sequences per species offers the possibility for developing distance determinations based on whole-genome information. The average nucleotide identity (ANI), calculated from pair-wise comparisons of all sequences shared between two given strains, has been proposed as the new metrics for bacterial species definition and classification. Results: In this study, we developed the web version of ANItools (http://ani.mypathogen.cn/), which helps users directly get ANI values from online sources. A database covering ANI values of any two strains in a genus was also included (2773 strains, 1487 species and 668 genera). Importantly, ANItools web can automatically run genome comparison between the input genomic sequence and data sequences (Genus and Species levels), and generate a graphical report for ANI calculation results. Conclusion: ANItools web is useful for defining the relationship between bacterial strains, further contributing to the classification and identification of bacterial species using genome data. Database URL: http://ani.mypathogen.cn/ Oxford University Press 2016-06-05 /pmc/articles/PMC4911789/ /pubmed/27270714 http://dx.doi.org/10.1093/database/baw084 Text en © The Author(s) 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Tool
Han, Na
Qiang, Yujun
Zhang, Wen
ANItools web: a web tool for fast genome comparison within multiple bacterial strains
title ANItools web: a web tool for fast genome comparison within multiple bacterial strains
title_full ANItools web: a web tool for fast genome comparison within multiple bacterial strains
title_fullStr ANItools web: a web tool for fast genome comparison within multiple bacterial strains
title_full_unstemmed ANItools web: a web tool for fast genome comparison within multiple bacterial strains
title_short ANItools web: a web tool for fast genome comparison within multiple bacterial strains
title_sort anitools web: a web tool for fast genome comparison within multiple bacterial strains
topic Database Tool
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911789/
https://www.ncbi.nlm.nih.gov/pubmed/27270714
http://dx.doi.org/10.1093/database/baw084
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