SHAPE-guided RNA structure homology search and motif discovery.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
31 03 2022
31 03 2022
Historique:
received:
10
12
2021
accepted:
11
03
2022
entrez:
1
4
2022
pubmed:
2
4
2022
medline:
5
4
2022
Statut:
epublish
Résumé
The rapidly growing popularity of RNA structure probing methods is leading to increasingly large amounts of available RNA structure information. This demands the development of efficient tools for the identification of RNAs sharing regions of structural similarity by direct comparison of their reactivity profiles, hence enabling the discovery of conserved structural features. We here introduce SHAPEwarp, a largely sequence-agnostic SHAPE-guided algorithm for the identification of structurally-similar regions in RNA molecules. Analysis of Dengue, Zika and coronavirus genomes recapitulates known regulatory RNA structures and identifies novel highly-conserved structural elements. This work represents a preliminary step towards the model-free search and identification of shared and conserved RNA structural features within transcriptomes.
Identifiants
pubmed: 35361788
doi: 10.1038/s41467-022-29398-y
pii: 10.1038/s41467-022-29398-y
pmc: PMC8971488
doi:
Substances chimiques
RNA, Guide
0
RNA
63231-63-0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1722Informations de copyright
© 2022. The Author(s).
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