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 a Jiří FAJKUS

Základní údaje

Originální název

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

Autoři

KILAR, Agata Magdalena (616 Polsko, domácí), Petr FAJKUS (203 Česká republika, domácí) a Jiří FAJKUS (203 Česká republika, garant, domácí)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10602 Biology , Evolutionary biology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 9.200 v roce 2022

Kód RIV

RIV/00216224:14740/23:00133555

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1093/gigascience/giad080

UT WoS

001176292300001

Klíčová slova anglicky

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

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 9. 10. 2024 12:50, Mgr. Eva Dubská

Anotace

V originále

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.

Návaznosti

GX20-01331X, projekt VaV

Název: Biogeneze a evoluce telomerázy u rostlin

Investor: Grantová agentura ČR, Biogenesis and evolution of telomerase in plants

LM2018131, projekt VaV

Název: Česká národní infrastruktura pro biologická data (Akronym: ELIXIR-CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Česká národní infrastruktura pro biologická data

LM2018140, projekt VaV

Název: e-Infrastruktura CZ (Akronym: e-INFRA CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, e-Infrastruktura CZ

52210685, interní kód MU

Název: Visegrad Scholarship Agata Kilar

Investor: Mezinárodní visegrádský fond (IVF), Visegrad Scholarship Agata Kilar

Citovat

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

@article{2374665,
   author = {Kilar, Agata Magdalena and Fajkus, Petr and Fajkus, Jiří},
   article_number = {October 2023},
   doi = {http://dx.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 a Jiří FAJKUS. GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context. \textit{GigaScience}. Oxford University Press, 2023, roč.~12, October 2023, s.~1-9. ISSN~2047-217X. Dostupné z: https://dx.doi.org/10.1093/gigascience/giad080.

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