Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots.

Background: Structured non-coding RNAs play many different roles in the cells, but the annotation of these RNAs is lacking even within the human genome. The currently available computational tools are either too computationally heavy for use in full genomic screens or rely on pre-aligned sequences.

Methods: Here we present a fast and efficient method, DotcodeR, for detecting structurally similar RNAs in genomic sequences by comparing their corresponding coarse-grained secondary structure dot plots at string level. This allows us to perform an all-against-all scan of all window pairs from two genomes without alignment.

Results: Our computational experiments with simulated data and real chromosomes demonstrate that the presented method has good sensitivity.

Conclusions: DotcodeR can be useful as a pre-filter in a genomic comparative scan for structured RNAs.