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

Tongchuan Zhang | Zendy; Jaswinder Singh | Zendy; Thomas Litfin | Zendy; Jian Zhan | Zendy; Kuldip K. Paliwal | Zendy; Yaoqi Zhou | Zendy

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

Author(s) -

Tongchuan Zhang,

Jaswinder Singh,

Thomas Litfin,

Jian Zhan,

Kuldip K. Paliwal,

Yaoqi Zhou

Publication year - 2021

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btab391

Subject(s) - computer science , pipeline (software) , rna , computational biology , nucleic acid structure , nucleic acid secondary structure , protein secondary structure , pseudoknot , folding (dsp implementation) , data mining , bioinformatics , biology , genetics , gene , biochemistry , programming language , engineering , electrical engineering

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.

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