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. 2023 Sep 2;39(9):btad549.
doi: 10.1093/bioinformatics/btad549.

FunTaxIS-lite: a simple and light solution to investigate protein functions in all living organisms

Federico Bianca  1 , Emilio Ispano  1 , Ermanno Gazzola  1 , Enrico Lavezzo  1 , Paolo Fontana  2 , Stefano Toppo  1
Affiliations

FunTaxIS-lite: a simple and light solution to investigate protein functions in all living organisms

Federico Bianca et al. Bioinformatics. .

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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Conflict of interest statement

None declared.

Figures

Figure 1.
Figure 1.
Comparison of evaluation metrics of FunTaxIS-lite and PANNZER. (A) This panel shows the performances for the species P.fluorescens SBW25 (tax ID: 216595). We have evaluated wFmax for each subontology (BP, CC, and MF) starting from the GO terms extracted by the protein hits found by DIAMOND (dashed line) and Argot (solid line). Performances have been evaluated without filtering (unfilt) and using both FunTaxIS-lite (FT) and PANNZER (PZ) taxonomic constraints. In Panel B, the Smin evaluation is reported for each subontology.
See this image and copyright information in PMC

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