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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F23%3A00604134" target="_blank" >RIV/68081707:_____/23:00604134 - isvavai.cz</a>

Alternative codes found

RIV/00216224:14740/23:00133555

Result on the web

<a href="https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad080/7319579?login=true" target="_blank" >https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad080/7319579?login=true</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/gigascience/giad080" target="_blank" >10.1093/gigascience/giad080</a>

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.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10608 - Biochemistry and molecular biology

Project

—

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2023

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

GigaScience

ISSN

2047-217X

e-ISSN

2047-217X

Volume of the periodical

12

Issue of the periodical within the volume

September

Country of publishing house

GB - UNITED KINGDOM

Number of pages

9

Pages from-to

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UT code for WoS article

001176292300001

EID of the result in the Scopus database

2-s2.0-85174750628