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TAGOPSIN: collating taxa-specific gene and protein functional and structural information

BACKGROUND: The wealth of biological information available nowadays in public databases has triggered an unprecedented rise in multi-database search and data retrieval for obtaining detailed information about key functional and structural entities. This concerns investigations ranging from gene or g...

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Autores principales: Bundhoo, Eshan, Ghoorah, Anisah W., Jaufeerally-Fakim, Yasmina
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8541804/
https://www.ncbi.nlm.nih.gov/pubmed/34688246
http://dx.doi.org/10.1186/s12859-021-04429-5
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author Bundhoo, Eshan
Ghoorah, Anisah W.
Jaufeerally-Fakim, Yasmina
author_facet Bundhoo, Eshan
Ghoorah, Anisah W.
Jaufeerally-Fakim, Yasmina
author_sort Bundhoo, Eshan
collection PubMed
description BACKGROUND: The wealth of biological information available nowadays in public databases has triggered an unprecedented rise in multi-database search and data retrieval for obtaining detailed information about key functional and structural entities. This concerns investigations ranging from gene or genome analysis to protein structural analysis. However, the retrieval of interconnected data from a number of different databases is very often done repeatedly in an unsystematic way. RESULTS: Here, we present TAxonomy, Gene, Ontology, Protein, Structure INtegrated (TAGOPSIN), a command line program written in Java for rapid and systematic retrieval of select data from seven of the most popular public biological databases relevant to comparative genomics and protein structure studies. The program allows a user to retrieve organism-centred data and assemble them in a single data warehouse which constitutes a useful resource for several biological applications. TAGOPSIN was tested with a number of organisms encompassing eukaryotes, prokaryotes and viruses. For example, it successfully integrated data for about 17,000 UniProt entries of Homo sapiens and 21 UniProt entries of human coronavirus. CONCLUSION: TAGOPSIN demonstrates efficient data integration whereby manipulation of interconnected data is more convenient than doing multi-database queries. The program facilitates for instance interspecific comparative analyses of protein-coding genes in a molecular evolutionary study, or identification of taxa-specific protein domains and three-dimensional structures. TAGOPSIN is available as a JAR file at https://github.com/ebundhoo/TAGOPSIN and is released under the GNU General Public License. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04429-5.
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spelling pubmed-85418042021-10-25 TAGOPSIN: collating taxa-specific gene and protein functional and structural information Bundhoo, Eshan Ghoorah, Anisah W. Jaufeerally-Fakim, Yasmina BMC Bioinformatics Software BACKGROUND: The wealth of biological information available nowadays in public databases has triggered an unprecedented rise in multi-database search and data retrieval for obtaining detailed information about key functional and structural entities. This concerns investigations ranging from gene or genome analysis to protein structural analysis. However, the retrieval of interconnected data from a number of different databases is very often done repeatedly in an unsystematic way. RESULTS: Here, we present TAxonomy, Gene, Ontology, Protein, Structure INtegrated (TAGOPSIN), a command line program written in Java for rapid and systematic retrieval of select data from seven of the most popular public biological databases relevant to comparative genomics and protein structure studies. The program allows a user to retrieve organism-centred data and assemble them in a single data warehouse which constitutes a useful resource for several biological applications. TAGOPSIN was tested with a number of organisms encompassing eukaryotes, prokaryotes and viruses. For example, it successfully integrated data for about 17,000 UniProt entries of Homo sapiens and 21 UniProt entries of human coronavirus. CONCLUSION: TAGOPSIN demonstrates efficient data integration whereby manipulation of interconnected data is more convenient than doing multi-database queries. The program facilitates for instance interspecific comparative analyses of protein-coding genes in a molecular evolutionary study, or identification of taxa-specific protein domains and three-dimensional structures. TAGOPSIN is available as a JAR file at https://github.com/ebundhoo/TAGOPSIN and is released under the GNU General Public License. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04429-5. BioMed Central 2021-10-23 /pmc/articles/PMC8541804/ /pubmed/34688246 http://dx.doi.org/10.1186/s12859-021-04429-5 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Bundhoo, Eshan
Ghoorah, Anisah W.
Jaufeerally-Fakim, Yasmina
TAGOPSIN: collating taxa-specific gene and protein functional and structural information
title TAGOPSIN: collating taxa-specific gene and protein functional and structural information
title_full TAGOPSIN: collating taxa-specific gene and protein functional and structural information
title_fullStr TAGOPSIN: collating taxa-specific gene and protein functional and structural information
title_full_unstemmed TAGOPSIN: collating taxa-specific gene and protein functional and structural information
title_short TAGOPSIN: collating taxa-specific gene and protein functional and structural information
title_sort tagopsin: collating taxa-specific gene and protein functional and structural information
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8541804/
https://www.ncbi.nlm.nih.gov/pubmed/34688246
http://dx.doi.org/10.1186/s12859-021-04429-5
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