GERONIMO: A tool for systematic retrieval of structural RNAs in
a broad evolutionary context

J 2023

GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context

KILAR, Agata Magdalena; Petr FAJKUS and Jiří FAJKUS

Basic information

Original name

GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context

Authors

KILAR, Agata Magdalena; Petr FAJKUS and Jiří FAJKUS

Edition

GigaScience, Oxford University Press, 2023, 2047-217X

Other information

Language

English

Type of outcome

Article in a journal

Field of Study

10602 Biology , Evolutionary biology

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

is not subject to a state or trade secret

References:

URL

Impact factor

Impact factor: 11.800

RIV identification code

RIV/00216224:14740/23:00133555

Organization unit

Central European Institute of Technology

DOI

https://doi.org/10.1093/gigascience/giad080

UT WoS

001176292300001

EID Scopus

2-s2.0-85174750628

Keywords in English

evolution; high-throughput pipeline; sequence homology searches; Snakemake

Abstract

In the original language

Background: While web-based tools such as BLAST have made identifying conserved gene homologs appear easy, genes with variable sequences pose significant challenges. Functionally important noncoding RNAs (ncRNA) often show low sequence conservation due to genetic variations, including insertions and deletions. Rather than conserved sequences, these RNAs possess highly conserved structural features across a broad phylogenetic range. Such features can be identified using the covariance models approach, which combines sequence alignment with a secondary RNA structure consensus. However, running standard implementation of that approach (Infernal) requires advanced bioinformatics knowledge compared to user-friendly web services like BLAST. The issue is partially addressed by RNAcentral, which can be used to search for homologs across a broad range of ncRNA sequence collections from diverse organisms but not across the genome assemblies. Results: Here, we present GERONIMO, which conducts evolutionary searches across hundreds of genomes in a fully automated way. It provides results extended with taxonomy context, as summary tables and visualizations, to facilitate analysis for user convenience. Additionally, GERONIMO supplements homologous sequences with genomic regions to analyze promoter motifs or gene collinearity, enhancing the validation of results. Conclusion: GERONIMO, built using Snakemake, has undergone extensive testing on hundreds of genomes, establishing itself as a valuable tool in the identification of ncRNA homologs across diverse taxonomic groups. Consequently, GERONIMO facilitates the investigation of the evolutionary patterns of functionally significant ncRNA players, whose understanding has previously been limited to individual organisms and close relatives.

Links

GX20-01331X, research and development project

Name: Biogeneze a evoluce telomerázy u rostlin

Investor: Czech Science Foundation

LM2018131, research and development project

Name: Česká národní infrastruktura pro biologická data (Acronym: ELIXIR-CZ)

Investor: Ministry of Education, Youth and Sports of the CR, Czech National Infrastructure for Biological Data

LM2018140, research and development project

Name: e-Infrastruktura CZ (Acronym: e-INFRA CZ)

Investor: Ministry of Education, Youth and Sports of the CR

52210685, interní kód MU

Name: Visegrad Scholarship Agata Kilar

Investor: International Visegrad Fund (IVF), Visegrad Scholarship Agata Kilar

Cite

KILAR, Agata Magdalena; Petr FAJKUS and Jiří FAJKUS. GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context. GigaScience. Oxford University Press, 2023, vol. 12, October 2023, p. 1-9. ISSN 2047-217X. Available from: https://doi.org/10.1093/gigascience/giad080.

@article{2374665,
   author = {Kilar, Agata Magdalena and Fajkus, Petr and Fajkus, Jiří},
   article_number = {October 2023},
   doi = {https://doi.org/10.1093/gigascience/giad080},
   keywords = {evolution; high-throughput pipeline; sequence homology searches; Snakemake},
   language = {eng},
   issn = {2047-217X},
   journal = {GigaScience},
   title = {GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context},
   url = {https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad080/7319579},
   volume = {12},
   year = {2023}
}

TY  - JOUR
ID  - 2374665
AU  - Kilar, Agata Magdalena - Fajkus, Petr - Fajkus, Jiří
PY  - 2023
TI  - GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context
JF  - GigaScience
VL  - 12
IS  - October 2023
SP  - 1-9
EP  - 1-9
PB  - Oxford University Press
SN  - 2047217X
KW  - evolution
KW  - high-throughput pipeline
KW  - sequence homology searches
KW  - Snakemake
UR  - https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad080/7319579
N2  - Background: While web-based tools such as BLAST have made identifying conserved gene homologs appear easy, genes with variable sequences pose significant challenges. Functionally important noncoding RNAs (ncRNA) often show low sequence conservation due to genetic variations, including insertions and deletions. Rather than conserved sequences, these RNAs possess highly conserved structural features across a broad phylogenetic range. Such features can be identified using the covariance models approach, which combines sequence alignment with a secondary RNA structure consensus. However, running standard implementation of that approach (Infernal) requires advanced bioinformatics knowledge compared to user-friendly web services like BLAST. The issue is partially addressed by RNAcentral, which can be used to search for homologs across a broad range of ncRNA sequence collections from diverse organisms but not across the genome assemblies. Results: Here, we present GERONIMO, which conducts evolutionary searches across hundreds of genomes in a fully automated way. It provides results extended with taxonomy context, as summary tables and visualizations, to facilitate analysis for user convenience. Additionally, GERONIMO supplements homologous sequences with genomic regions to analyze promoter motifs or gene collinearity, enhancing the validation of results. Conclusion: GERONIMO, built using Snakemake, has undergone extensive testing on hundreds of genomes, establishing itself as a valuable tool in the identification of ncRNA homologs across diverse taxonomic groups. Consequently, GERONIMO facilitates the investigation of the evolutionary patterns of functionally significant ncRNA players, whose understanding has previously been limited to individual organisms and close relatives.
ER  -

KILAR, Agata Magdalena; Petr FAJKUS and Jiří FAJKUS. GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context. \textit{GigaScience}. Oxford University Press, 2023, vol.~12, October 2023, p.~1-9. ISSN~2047-217X. Available from: https://doi.org/10.1093/gigascience/giad080.

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