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Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology

Summary: We present Vacceed, a highly configurable and scalable framework designed to automate the process of high-throughput in silico vaccine candidate discovery for eukaryotic pathogens. Given thousands of protein sequences from the target pathogen as input, the main output is a ranked list of pr...

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Detalles Bibliográficos
Autores principales: Goodswen, Stephen J., Kennedy, Paul J., Ellis, John T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4207429/
https://www.ncbi.nlm.nih.gov/pubmed/24790156
http://dx.doi.org/10.1093/bioinformatics/btu300
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author Goodswen, Stephen J.
Kennedy, Paul J.
Ellis, John T.
author_facet Goodswen, Stephen J.
Kennedy, Paul J.
Ellis, John T.
author_sort Goodswen, Stephen J.
collection PubMed
description Summary: We present Vacceed, a highly configurable and scalable framework designed to automate the process of high-throughput in silico vaccine candidate discovery for eukaryotic pathogens. Given thousands of protein sequences from the target pathogen as input, the main output is a ranked list of protein candidates determined by a set of machine learning algorithms. Vacceed has the potential to save time and money by reducing the number of false candidates allocated for laboratory validation. Vacceed, if required, can also predict protein sequences from the pathogen’s genome. Availability and implementation: Vacceed is tested on Linux and can be freely downloaded from https://github.com/sgoodswe/vacceed/releases (includes a worked example with sample data). Vacceed User Guide can be obtained from https://github.com/sgoodswe/vacceed. Contact: John.Ellis@uts.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-42074292014-10-28 Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology Goodswen, Stephen J. Kennedy, Paul J. Ellis, John T. Bioinformatics Applications Notes Summary: We present Vacceed, a highly configurable and scalable framework designed to automate the process of high-throughput in silico vaccine candidate discovery for eukaryotic pathogens. Given thousands of protein sequences from the target pathogen as input, the main output is a ranked list of protein candidates determined by a set of machine learning algorithms. Vacceed has the potential to save time and money by reducing the number of false candidates allocated for laboratory validation. Vacceed, if required, can also predict protein sequences from the pathogen’s genome. Availability and implementation: Vacceed is tested on Linux and can be freely downloaded from https://github.com/sgoodswe/vacceed/releases (includes a worked example with sample data). Vacceed User Guide can be obtained from https://github.com/sgoodswe/vacceed. Contact: John.Ellis@uts.edu.au Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2014-08-15 2014-04-29 /pmc/articles/PMC4207429/ /pubmed/24790156 http://dx.doi.org/10.1093/bioinformatics/btu300 Text en © The Author 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Goodswen, Stephen J.
Kennedy, Paul J.
Ellis, John T.
Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology
title Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology
title_full Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology
title_fullStr Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology
title_full_unstemmed Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology
title_short Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology
title_sort vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4207429/
https://www.ncbi.nlm.nih.gov/pubmed/24790156
http://dx.doi.org/10.1093/bioinformatics/btu300
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