Bianca F, Ispano E, Gazzola E, Lavezzo E, Fontana P, Toppo S. FunTaxIS-lite: a simple and light solution to investigate protein functions in all living organisms.
Bioinformatics 2023;
39:btad549. [PMID:
37672040 PMCID:
PMC10500080 DOI:
10.1093/bioinformatics/btad549]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/27/2023] [Accepted: 09/05/2023] [Indexed: 09/07/2023] Open
Abstract
MOTIVATION
Defining the full domain of protein functions belonging to an organism is a complex challenge that is due to the huge heterogeneity of the taxonomy, where single or small groups of species can bear unique functional characteristics. FunTaxIS-lite provides a solution to this challenge by determining taxon-based constraints on Gene Ontology (GO) terms, which specify the functions that an organism can or cannot perform. The tool employs a set of rules to generate and spread the constraints across both the taxon hierarchy and the GO graph.
RESULTS
The taxon-based constraints produced by FunTaxIS-lite extend those provided by the Gene Ontology Consortium by an average of 300%. The implementation of these rules significantly reduces errors in function predictions made by automatic algorithms and can assist in correcting inconsistent protein annotations in databases.
AVAILABILITY AND IMPLEMENTATION
FunTaxIS-lite is available on https://www.medcomp.medicina.unipd.it/funtaxis-lite and from https://github.com/MedCompUnipd/FunTaxIS-lite.
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