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

Autor: Bundhoo E; Department of Agricultural and Food Science, Faculty of Agriculture, University of Mauritius, Reduit, 80837, Mauritius., Ghoorah AW; Department of Digital Technologies, Faculty of Information, Communication and Digital Technologies, University of Mauritius, Reduit, 80837, Mauritius. a.ghoorah@uom.ac.mu., Jaufeerally-Fakim Y; Department of Agricultural and Food Science, Faculty of Agriculture, University of Mauritius, Reduit, 80837, Mauritius.
Jazyk: angličtina
Zdroj: BMC bioinformatics [BMC Bioinformatics] 2021 Oct 23; Vol. 22 (1), pp. 517. Date of Electronic Publication: 2021 Oct 23.
DOI: 10.1186/s12859-021-04429-5
Abstrakt: 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.
(© 2021. The Author(s).)
Databáze: MEDLINE
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