RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis.

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

The accuracy of RNA secondary and tertiary structure prediction can be significantly improved by using structural restraints derived from evolutionary coupling or direct coupling analysis. Currently, these coupling analyses relied on manually curated multiple sequence alignments collected in the Rfam database, which contains 3016 families. By comparison, millions of non-coding RNA sequences are known. Here, we established RNAcmap, a fully automatic pipeline that enables evolutionary coupling analysis for any RNA sequences. The homology search was based on the covariance model built by INFERNAL according to two secondary structure predictors: a folding-based algorithm RNAfold and the latest deep-learning method SPOT-RNA.

Related collections

Author and article information

Journal

Journal ID (iso-abbrev): Bioinformatics

Title: Bioinformatics (Oxford, England)

Publisher: Oxford University Press (OUP)

ISSN (Electronic): 1367-4811

ISSN (Print): 1367-4803

Publication date (Electronic): Oct 25 2021

Volume: 37

Issue: 20

Affiliations

[1 ] Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr. Southport, Queensland 4222, Australia.

[2 ] Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, Queensland 4111, Australia.

[3 ] Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.

Article

Publisher Item ID: 6281070

DOI: 10.1093/bioinformatics/btab391

PubMed ID: 34021744

SO-VID: eed574e3-c82d-4d31-a456-03750211a6c8

History

Data availability:

Comments

Comment on this article

scite_

Cited by 10

See all cited by