Response to Tavares et al., "Covariation analysis with improved parameters reveals conservation in lncRNA structures"

Tavares conclusions depend on an assumption that the statistic they use (RAFS) is an appropriate measure of RNA base pair covariation, but RAFS was not designed to measure covariation alone. RAFS detects positive signals in common patterns of primary sequence conservation in absence of any covariation. To illustrate the severity of the problem, we show that Tavares analysis reports "significantly covarying base pairs" in 100% identical sequence alignments with no variation or covariation. We use Tavares sequence alignment of HOTAIR domain 1 as an example to show that the base pairs they identify as significantly covarying actually arise from primary sequence conservation patterns. Their analysis still reports similar numbers of "significant covarying" base pairs in a negative control in which we permute residues in independent alignment columns to destroy covariation. There remains no significant covariation support for evolutionarily conserved RNA structure in the HOTAIR lncRNA or other lncRNA structures and alignments we have analyzed.