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Updated: Jun 5, 2025
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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
Published on: February 10, 2023
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Revisiting the functional annotation of TriTryp using sequence similarity tools
Poorya Mirzavand Borujeni1, Reza Salavati1,2
1Institute of Parasitology, McGill University, Canada.
Heliyon
|December 6, 2024
Summary
Automated annotation tools like PANNZER2 improve gene function discovery in trypanosomatids. This study enhances functional annotation and identifies potential pseudogenes in key parasitic organisms.
Area of Science:
- Genomics and Bioinformatics
- Parasitology
- Molecular Biology
Background:
- Trypanosomatids cause significant human and livestock diseases.
- Many genes in trypanosomatids remain unannotated due to phylogenetic distance from model organisms.
- Automated functional annotation tools are crucial for efficient gene function discovery.
Purpose of the Study:
- To evaluate the effectiveness of the PANNZER2 tool for automated functional annotation in trypanosomatids.
- To identify limitations in existing annotation processes within databases like TriTrypDB.
- To develop methods for identifying potential pseudogenes in trypanosomatid genomes.
Main Methods:
- Applied PANNZER2 for sequence similarity-based functional annotation of genes in *Trypanosoma brucei*.
- Analyzed annotation gaps by comparing PANNZER2 results with TriTrypDB's automated annotations.
- Investigated gene sequences by adjusting open reading frames to assess sequence signature coverage.
- Extended the analysis to *Trypanosoma cruzi* and *Leishmania major*.
Main Results:
- PANNZER2 provided confident functional predictions for hypothetical proteins in *T. brucei*, highlighting gaps in current annotations.
- Pairwise sequence similarity alignment, even with stringent cutoffs, successfully annotated numerous proteins.
- Adjusting open reading frames revealed increased sequence signature coverage, suggesting potential pseudogenes.
- Attributed 2986, 3953, and 3798 new Gene Ontology (GO) terms to *T. brucei*, *T. cruzi*, and *L. major*, respectively.
- Identified 210, 239, and 29 genes with characteristics of pseudogenes in *T. brucei*, *T. cruzi*, and *L. major*.
Conclusions:
- Pairwise sequence similarity alignment is a valuable approach for improving automated functional gene annotation in trypanosomatids.
- The study identified a significant number of novel functional annotations and potential pseudogenes across multiple trypanosomatid species.
- A script was developed to aid researchers in identifying potential pseudogenes, advancing genomic analysis in these organisms.
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