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Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations

BACKGROUND: Here we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence...

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Autores principales: Leung, Elo, Huang, Amy, Cadag, Eithon, Montana, Aldrin, Soliman, Jan Lorenz, Zhou, Carol L. Ecale
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4721133/
https://www.ncbi.nlm.nih.gov/pubmed/26792120
http://dx.doi.org/10.1186/s12859-016-0887-y
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author Leung, Elo
Huang, Amy
Cadag, Eithon
Montana, Aldrin
Soliman, Jan Lorenz
Zhou, Carol L. Ecale
author_facet Leung, Elo
Huang, Amy
Cadag, Eithon
Montana, Aldrin
Soliman, Jan Lorenz
Zhou, Carol L. Ecale
author_sort Leung, Elo
collection PubMed
description BACKGROUND: Here we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. RESULTS: In this paper, we demonstrate the utility of PSAT by annotating the predicted peptide gene products of Herbaspirillum sp. strain RV1423, importing the results of PSAT into EC2KEGG, and using the resulting functional comparisons to identify a putative catabolic pathway, thereby distinguishing RV1423 from a well annotated Herbaspirillum species. This analysis demonstrates that high-throughput enzyme predictions, provided by PSAT processing, can be used to identify metabolic potential in an otherwise poorly annotated genome. CONCLUSIONS: PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/. PSAT stands apart from other sequence-based genome annotation systems in providing a high-throughput platform for rapid de novo enzyme predictions and sequence annotations over large input protein sequence data sets in FASTA. PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single genome. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-0887-y) contains supplementary material, which is available to authorized users.
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spelling pubmed-47211332016-01-22 Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations Leung, Elo Huang, Amy Cadag, Eithon Montana, Aldrin Soliman, Jan Lorenz Zhou, Carol L. Ecale BMC Bioinformatics Software BACKGROUND: Here we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. RESULTS: In this paper, we demonstrate the utility of PSAT by annotating the predicted peptide gene products of Herbaspirillum sp. strain RV1423, importing the results of PSAT into EC2KEGG, and using the resulting functional comparisons to identify a putative catabolic pathway, thereby distinguishing RV1423 from a well annotated Herbaspirillum species. This analysis demonstrates that high-throughput enzyme predictions, provided by PSAT processing, can be used to identify metabolic potential in an otherwise poorly annotated genome. CONCLUSIONS: PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/. PSAT stands apart from other sequence-based genome annotation systems in providing a high-throughput platform for rapid de novo enzyme predictions and sequence annotations over large input protein sequence data sets in FASTA. PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single genome. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-0887-y) contains supplementary material, which is available to authorized users. BioMed Central 2016-01-20 /pmc/articles/PMC4721133/ /pubmed/26792120 http://dx.doi.org/10.1186/s12859-016-0887-y Text en © Leung et al. 2016 Open AccessThis article is distributed 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 you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Leung, Elo
Huang, Amy
Cadag, Eithon
Montana, Aldrin
Soliman, Jan Lorenz
Zhou, Carol L. Ecale
Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations
title Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations
title_full Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations
title_fullStr Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations
title_full_unstemmed Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations
title_short Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations
title_sort protein sequence annotation tool (psat): a centralized web-based meta-server for high-throughput sequence annotations
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4721133/
https://www.ncbi.nlm.nih.gov/pubmed/26792120
http://dx.doi.org/10.1186/s12859-016-0887-y
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