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

Kód výsledku v 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>

Nalezeny alternativní kódy

RIV/00216224:14740/23:00133555

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10608 - Biochemistry and molecular biology

Projekt

—

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2023

Kód důvěrnosti údajů

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

Název periodika

GigaScience

ISSN

2047-217X

e-ISSN

2047-217X

Svazek periodika

12

Číslo periodika v rámci svazku

September

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

9

Strana od-do

—

Kód UT WoS článku

001176292300001

EID výsledku v databázi Scopus

2-s2.0-85174750628