rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F19%3A00518202" target="_blank" >RIV/61388971:_____/19:00518202 - isvavai.cz</a>

Alternative codes found

RIV/00216208:11320/19:10409403

Result on the web

<a href="https://academic.oup.com/database/article/doi/10.1093/database/baz047/5479229" target="_blank" >https://academic.oup.com/database/article/doi/10.1093/database/baz047/5479229</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/database/baz047" target="_blank" >10.1093/database/baz047</a>

Result language

angličtina

Original language name

rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots

Original language description

Secondary data structure of RNA molecules provides insights into the identity and function of RNAs. With RNAs readily sequenced, the question of their structural characterization is increasingly important. However, RNA structure is difficult to acquire. Its experimental identification is extremely technically demanding, while computational prediction is not accurate enough, especially for large structures of long sequences. We address this difficult situation with rPredictorDB, a predictive database of RNA secondary structures that aims to form a middle ground between experimentally identified structures in PDB and predicted consensus secondary structures in Rfam. The database contains individual secondary structures predicted using a tool for template-based prediction of RNA secondary structure for the homologs of the RNA families with at least one homolog with experimentally solved structure. Experimentally identified structures are used as the structural templates and thus the prediction has higher reliability than de novo predictions in Rfam. The sequences are downloaded from public resources. So far rPredictorDB covers 7365 RNAs with their secondary structures. Plots of the secondary structures use the Traveler package for readable display of RNAs with long sequences and complex structures, such as ribosomal RNAs. The RNAs in the output of rPredictorDB are extensively annotated and can be viewed, browsed, searched and downloaded according to taxonomic, sequence and structure data. Additionally, structure of user-provided sequences can be predicted using the templates stored in rPredictorDB.

Czech name

—

Czech description

—

Type

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

CEP classification

—

OECD FORD branch

10602 - Biology (theoretical, mathematical, thermal, cryobiology, biological rhythm), Evolutionary biology

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2019

Confidentiality

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

Name of the periodical

Database

ISSN

1758-0463

e-ISSN

—

Volume of the periodical

2019

Issue of the periodical within the volume

APR 25

Country of publishing house

GB - UNITED KINGDOM

Number of pages

9

Pages from-to

baz047

UT code for WoS article

000469885500001

EID of the result in the Scopus database

2-s2.0-85065443404