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Updated: Jul 13, 2025
07:09
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
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GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context
Agata M Kilar1,2, Petr Fajkus1,3, Jiří Fajkus1,2,3
1Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic.
Gigascience
|October 17, 2023
Summary
Identifying noncoding RNA (ncRNA) homologs is challenging due to low sequence conservation. GERONIMO offers an automated solution for evolutionary ncRNA searches across genomes, aiding evolutionary pattern investigation.
Area of Science:
- Bioinformatics
- Genomics
- Molecular Biology
Background:
- Noncoding RNAs (ncRNAs) often lack sequence conservation, complicating homolog identification.
- Conserved structural features, not sequences, are key for identifying evolutionarily distant ncRNAs.
- Existing tools like Infernal require advanced bioinformatics skills, while RNAcentral has limitations in genome-wide searches.
Purpose of the Study:
- To present GERONIMO, an automated tool for large-scale, evolutionary ncRNA homolog searches.
- To provide user-friendly analysis of ncRNA evolution across diverse organisms and genomes.
Main Methods:
- Development of GERONIMO using the Snakemake workflow management system.
- Automated, genome-wide evolutionary searches for ncRNA homologs.
- Integration of taxonomic context, visualizations, and genomic region analysis.
Main Results:
- GERONIMO enables automated, comprehensive evolutionary searches across hundreds of genomes.
- Results include taxonomic context, summary tables, and visualizations for enhanced usability.
- Genomic regions surrounding homologs are provided for promoter motif and gene collinearity analysis.
Conclusions:
- GERONIMO is a robust tool for identifying ncRNA homologs across diverse taxonomic groups.
- Facilitates the study of evolutionary patterns of functionally significant ncRNAs.
- Overcomes limitations of previous methods for large-scale ncRNA evolutionary analysis.
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