TAGOPSIN: collating taxa-specific gene and protein functional and structural information
Abstract 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 g...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-10-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-021-04429-5 |
| _version_ | 1819292640897662976 |
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| author | Eshan Bundhoo Anisah W. Ghoorah Yasmina Jaufeerally-Fakim |
| author_facet | Eshan Bundhoo Anisah W. Ghoorah Yasmina Jaufeerally-Fakim |
| author_sort | Eshan Bundhoo |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-24T03:57:45Z |
| format | Article |
| id | doaj.art-3810032c95bb48aea0147bd47c707041 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-24T03:57:45Z |
| publishDate | 2021-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-3810032c95bb48aea0147bd47c7070412022-12-21T17:16:24ZengBMCBMC Bioinformatics1471-21052021-10-0122111510.1186/s12859-021-04429-5TAGOPSIN: collating taxa-specific gene and protein functional and structural informationEshan Bundhoo0Anisah W. Ghoorah1Yasmina Jaufeerally-Fakim2Department of Agricultural and Food Science, Faculty of Agriculture, University of MauritiusDepartment of Digital Technologies, Faculty of Information, Communication and Digital Technologies, University of MauritiusDepartment of Agricultural and Food Science, Faculty of Agriculture, University of MauritiusAbstract 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.https://doi.org/10.1186/s12859-021-04429-5Comparative genomicsData integrationData retrievalDatabaseObject-oriented biology |
| spellingShingle | Eshan Bundhoo Anisah W. Ghoorah Yasmina Jaufeerally-Fakim TAGOPSIN: collating taxa-specific gene and protein functional and structural information BMC Bioinformatics Comparative genomics Data integration Data retrieval Database Object-oriented biology |
| 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 | Comparative genomics Data integration Data retrieval Database Object-oriented biology |
| url | https://doi.org/10.1186/s12859-021-04429-5 |
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