SPDB: a specialized database and web-based analysis platform for swine pathogens

The rapid and accurate diagnosis of swine diseases is indispensable for reducing their negative impacts on the pork industry. Next-generation sequencing (NGS) is a promising diagnostic tool for swine diseases. To support the application of NGS in the diagnosis of swine disease, we established the Sw...

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Detalles Bibliográficos
Autores principales: Wang, Xiaoru, Liu, Zongbao, Li, Xiaoying, Li, Danwei, Cai, Jiayu, Yan, He
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Original Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7409514/
https://www.ncbi.nlm.nih.gov/pubmed/32761141
http://dx.doi.org/10.1093/database/baaa063
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author Wang, Xiaoru
Liu, Zongbao
Li, Xiaoying
Li, Danwei
Cai, Jiayu
Yan, He
author_facet Wang, Xiaoru
Liu, Zongbao
Li, Xiaoying
Li, Danwei
Cai, Jiayu
Yan, He
author_sort Wang, Xiaoru
collection PubMed
description The rapid and accurate diagnosis of swine diseases is indispensable for reducing their negative impacts on the pork industry. Next-generation sequencing (NGS) is a promising diagnostic tool for swine diseases. To support the application of NGS in the diagnosis of swine disease, we established the Swine Pathogen Database (SPDB). The SPDB represents the first comprehensive and highly specialized database and analysis platform for swine pathogens. The current version features an online genome search tool, which now contains 26 148 genomes of swine, swine pathogens and phylogenetically related species. This database offers a comprehensive bioinformatics analysis pipeline for the identification of 4403 swine pathogens and their related species in clinical samples, based on targeted 16S rRNA gene sequencing and metagenomic NGS data. The SPDB provides a powerful and user-friendly service for veterinarians and researchers to support the applications of NGS in swine disease research. Database URL: http://spdatabase.com:2080/
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spelling pubmed-74095142020-08-10 SPDB: a specialized database and web-based analysis platform for swine pathogens Wang, Xiaoru Liu, Zongbao Li, Xiaoying Li, Danwei Cai, Jiayu Yan, He Database (Oxford) Original Article The rapid and accurate diagnosis of swine diseases is indispensable for reducing their negative impacts on the pork industry. Next-generation sequencing (NGS) is a promising diagnostic tool for swine diseases. To support the application of NGS in the diagnosis of swine disease, we established the Swine Pathogen Database (SPDB). The SPDB represents the first comprehensive and highly specialized database and analysis platform for swine pathogens. The current version features an online genome search tool, which now contains 26 148 genomes of swine, swine pathogens and phylogenetically related species. This database offers a comprehensive bioinformatics analysis pipeline for the identification of 4403 swine pathogens and their related species in clinical samples, based on targeted 16S rRNA gene sequencing and metagenomic NGS data. The SPDB provides a powerful and user-friendly service for veterinarians and researchers to support the applications of NGS in swine disease research. Database URL: http://spdatabase.com:2080/ Oxford University Press 2020-08-06 /pmc/articles/PMC7409514/ /pubmed/32761141 http://dx.doi.org/10.1093/database/baaa063 Text en © The Author(s) 2020. 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 Original Article
Wang, Xiaoru
Liu, Zongbao
Li, Xiaoying
Li, Danwei
Cai, Jiayu
Yan, He
SPDB: a specialized database and web-based analysis platform for swine pathogens
title SPDB: a specialized database and web-based analysis platform for swine pathogens
title_full SPDB: a specialized database and web-based analysis platform for swine pathogens
title_fullStr SPDB: a specialized database and web-based analysis platform for swine pathogens
title_full_unstemmed SPDB: a specialized database and web-based analysis platform for swine pathogens
title_short SPDB: a specialized database and web-based analysis platform for swine pathogens
title_sort spdb: a specialized database and web-based analysis platform for swine pathogens
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7409514/
https://www.ncbi.nlm.nih.gov/pubmed/32761141
http://dx.doi.org/10.1093/database/baaa063
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