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Estimating the power of sequence covariation for detecting conserved RNA structure.

ABSTRACT: Pairwise sequence covariations are a signal of conserved RNA secondary structure. We describe a method for distinguishing when lack of covariation signal can be taken as evidence against a conserved RNA structure, as opposed to when a sequence alignment merely has insufficient variation to detect covariations. We find that alignments for several long non-coding RNAs previously shown to lack covariation support do have adequate covariation detection power, providing additional evidence against their proposed conserved structures. AVAILABILITY AND IMPLEMENTATION:The R-scape web server is at eddylab.org/R-scape, with a link to download the source code. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

SUBMITTER: Rivas E

PROVIDER: S-EPMC7214042 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Estimating the power of sequence covariation for detecting conserved RNA structure.

Rivas Elena E Clements Jody J Eddy Sean R SR

Bioinformatics (Oxford, England) 20200501 10

Pairwise sequence covariations are a signal of conserved RNA secondary structure. We describe a method for distinguishing when lack of covariation signal can be taken as evidence against a conserved RNA structure, as opposed to when a sequence alignment merely has insufficient variation to detect covariations. We find that alignments for several long non-coding RNAs previously shown to lack covariation support do have adequate covariation detection power, providing additional evidence against th ...[more]

PMID: 32031582

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