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

ABSTRACT:

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,

SUBMITTER: Kilar AM 

PROVIDER: S-EPMC10580375 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature