GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F23%3A00133555" target="_blank" >RIV/00216224:14740/23:00133555 - isvavai.cz</a>
Result on the web
<a href="https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad080/7319579" target="_blank" >https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad080/7319579</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1093/gigascience/giad080" target="_blank" >10.1093/gigascience/giad080</a>
Alternative languages
Result language
angličtina
Original language name
GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context
Original language description
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.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10602 - Biology (theoretical, mathematical, thermal, cryobiology, biological rhythm), Evolutionary biology
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach
Others
Publication year
2023
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
GigaScience
ISSN
2047-217X
e-ISSN
2047-217X
Volume of the periodical
12
Issue of the periodical within the volume
October 2023
Country of publishing house
GB - UNITED KINGDOM
Number of pages
9
Pages from-to
1-9
UT code for WoS article
001176292300001
EID of the result in the Scopus database
2-s2.0-85174750628