Protegen: a web-based protective antigen database and analysis system

Protective antigens are specifically targeted by the acquired immune response of the host and are able to induce protection in the host against infectious and non-infectious diseases. Protective antigens play important roles in vaccine development, as biological markers for disease diagnosis, and fo...

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Autores principales: Yang, Brian, Sayers, Samantha, Xiang, Zuoshuang, He, Yongqun
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013795/
https://www.ncbi.nlm.nih.gov/pubmed/20959289
http://dx.doi.org/10.1093/nar/gkq944
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author Yang, Brian
Sayers, Samantha
Xiang, Zuoshuang
He, Yongqun
author_facet Yang, Brian
Sayers, Samantha
Xiang, Zuoshuang
He, Yongqun
author_sort Yang, Brian
collection PubMed
description Protective antigens are specifically targeted by the acquired immune response of the host and are able to induce protection in the host against infectious and non-infectious diseases. Protective antigens play important roles in vaccine development, as biological markers for disease diagnosis, and for analysis of fundamental host immunity against diseases. Protegen is a web-based central database and analysis system that curates, stores and analyzes protective antigens. Basic antigen information and experimental evidence are curated from peer-reviewed articles. More detailed gene/protein information (e.g. DNA and protein sequences, and COG classification) are automatically extracted from existing databases using internally developed scripts. Bioinformatics programs are also applied to compute different antigen features, such as protein weight and pI, and subcellular localizations of bacterial proteins. Presently, 590 protective antigens have been curated against over 100 infectious diseases caused by pathogens and non-infectious diseases (including cancers and allergies). A user-friendly web query and visualization interface is developed for interactive protective antigen search. A customized BLAST sequence similarity search is also developed for analysis of new sequences provided by the users. To support data exchange, the information of protective antigens is stored in the Vaccine Ontology (VO) in OWL format and can also be exported to FASTA and Excel files. Protegen is publically available at http://www.violinet.org/protegen.
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spelling pubmed-30137952011-01-03 Protegen: a web-based protective antigen database and analysis system Yang, Brian Sayers, Samantha Xiang, Zuoshuang He, Yongqun Nucleic Acids Res Articles Protective antigens are specifically targeted by the acquired immune response of the host and are able to induce protection in the host against infectious and non-infectious diseases. Protective antigens play important roles in vaccine development, as biological markers for disease diagnosis, and for analysis of fundamental host immunity against diseases. Protegen is a web-based central database and analysis system that curates, stores and analyzes protective antigens. Basic antigen information and experimental evidence are curated from peer-reviewed articles. More detailed gene/protein information (e.g. DNA and protein sequences, and COG classification) are automatically extracted from existing databases using internally developed scripts. Bioinformatics programs are also applied to compute different antigen features, such as protein weight and pI, and subcellular localizations of bacterial proteins. Presently, 590 protective antigens have been curated against over 100 infectious diseases caused by pathogens and non-infectious diseases (including cancers and allergies). A user-friendly web query and visualization interface is developed for interactive protective antigen search. A customized BLAST sequence similarity search is also developed for analysis of new sequences provided by the users. To support data exchange, the information of protective antigens is stored in the Vaccine Ontology (VO) in OWL format and can also be exported to FASTA and Excel files. Protegen is publically available at http://www.violinet.org/protegen. Oxford University Press 2011-01 2010-10-19 /pmc/articles/PMC3013795/ /pubmed/20959289 http://dx.doi.org/10.1093/nar/gkq944 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Yang, Brian
Sayers, Samantha
Xiang, Zuoshuang
He, Yongqun
Protegen: a web-based protective antigen database and analysis system
title Protegen: a web-based protective antigen database and analysis system
title_full Protegen: a web-based protective antigen database and analysis system
title_fullStr Protegen: a web-based protective antigen database and analysis system
title_full_unstemmed Protegen: a web-based protective antigen database and analysis system
title_short Protegen: a web-based protective antigen database and analysis system
title_sort protegen: a web-based protective antigen database and analysis system
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013795/
https://www.ncbi.nlm.nih.gov/pubmed/20959289
http://dx.doi.org/10.1093/nar/gkq944
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