PT  - JOURNAL ARTICLE
AU  - Rafael C A Tavares
AU  - Anna Marie Pyle
AU  - Srinivas Somarowthu
TI  - Covariation analysis with improved parameters reveals conservation in lncRNA structures
AID  - 10.1101/364109
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 364109
4099  - http://biorxiv.org/content/early/2018/07/06/364109.short
4100  - http://biorxiv.org/content/early/2018/07/06/364109.full
AB  - The existence of phylogenetic covariation in base-pairing is strong evidence for functional elements of RNA structure, although available tools for identifying covariation are limited. R-scape is a recently developed program for prediction of covariation from sequence alignments, but it has limited utility on long RNAs, especially those of eukaryotic origin. Here we show that R-scape can be adapted for powerful prediction of covariation in long RNA molecules, including mammalian lncRNAs.