Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains.

ABSTRACT:

Motivation

Simultaneous alignment and folding (SA&F) of RNAs is the indispensable gold standard for inferring the structure of non-coding RNAs and their general analysis. The original algorithm, proposed by Sankoff, solves the theoretical problem exactly with a complexity of [Formula: see text] in the full energy model. Over the last two decades, several variants and improvements of the Sankoff algorithm have been proposed to reduce its extreme complexity by proposing simplified energy models or imposing restrictions on the predicted alignments.

Results

Here, we introduce a novel variant of Sankoff's algorithm that reconciles the simplifications of PMcomp, namely moving from the full energy model to a simpler base pair-based model, with the accuracy of the loop-based full en

SUBMITTER: Miladi M 

PROVIDER: S-EPMC7666477 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature