An Algorithm for Template-Based Prediction of Secondary Structures of Individual RNA Sequences

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F17%3A00480493" target="_blank" >RIV/61388971:_____/17:00480493 - isvavai.cz</a>

Result on the web

<a href="http://dx.doi.org/10.3389/fgene.2017.00147" target="_blank" >http://dx.doi.org/10.3389/fgene.2017.00147</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.3389/fgene.2017.00147" target="_blank" >10.3389/fgene.2017.00147</a>

Result language

angličtina

Original language name

An Algorithm for Template-Based Prediction of Secondary Structures of Individual RNA Sequences

Original language description

While understanding the structure of RNA molecules is vital for deciphering their functions, determining RNA structures experimentally is exceptionally hard. At the same time, extant approaches to computational RNA structure prediction have limited applicability and reliability. In this paper we provide a method to solve a simpler yet still biologically relevant problem: prediction of secondary RNA structure using structure of different molecules as a template. Our method identifies conserved and unconserved subsequences within an RNA molecule. For conserved subsequences, the template structure is directly transferred into the generated structure and combined with de-novo predicted structure for the unconserved subsequences with low evolutionary conservation. The method also determines, when the generated structure is unreliable. The method is validated using experimentally identified structures. The accuracy of the method exceeds that of classical prediction algorithms and constrained prediction methods. This is demonstrated by comparison using large number of heterogeneous RNAs. The presented method is fast and robust, and useful for various applications requiring knowledge of secondary structures of individual RNA sequences.

Czech name

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Czech description

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Type

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

CEP classification

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OECD FORD branch

10606 - Microbiology

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

2017

Confidentiality

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

Name of the periodical

Frontiers in genetics

ISSN

1664-8021

e-ISSN

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Volume of the periodical

8

Issue of the periodical within the volume

OCT 10

Country of publishing house

CH - SWITZERLAND

Number of pages

11

Pages from-to

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UT code for WoS article

000412633900001

EID of the result in the Scopus database

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