D-ORB: A Web Server to Extract Structural Features of Related But Unaligned RNA Sequences.
J Mol Biol
; 435(15): 168181, 2023 08 01.
Article
em En
| MEDLINE
| ID: mdl-37468182
ABSTRACT
Identifying the common structural elements of functionally related RNA sequences (family) is usually based on an alignment of the sequences, which is often subject to human bias and may not be accurate. The resulting covariance model (CM) provides probabilities for each base to covary with another, which allows to support evolutionarily the formation of double helical regions and possibly pseudoknots. The coexistence of alternative folds in RNA, resulting from its dynamic nature, may lead to the potential omission of motifs by CM. To overcome this limitation, we present D-ORB, a system of algorithms that identifies overrepresented motifs in the secondary conformational landscapes of a family when compared to those of unrelated sequences. The algorithms are bundled into an easy-to-use website allowing users to submit a family, and optionally provide unrelated sequences. D-ORB produces a non-pseudoknotted secondary structure based on the overrepresented motifs, a deep neural network classifier and two decision trees. When used to model an Rfam family, D-ORB fits overrepresented motifs in the corresponding Rfam structure; more than a hundred Rfam families have been modeled. The statistical approach behind D-ORB derives the structural composition of an RNA family, making it a valuable tool for analyzing and modeling it. Its easy-to-use interface and advanced algorithms make it an essential resource for researchers studying RNA structure. D-ORB is available at https//d-orb.major.iric.ca/.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
RNA
Tipo de estudo:
Prognostic_studies
Limite:
Humans
Idioma:
En
Revista:
J Mol Biol
Ano de publicação:
2023
Tipo de documento:
Article
País de afiliação:
Canadá