I have done de novo assembly of pair end raw read sequences and resulted transcripts sequences were separated based on coding potential into two categories: long non-coding RNA transcripts and coding RNA transcripts.I want to find how many of long non coding can make hairpin loop structure and how can I annotate these miRNA which are generated from long non coding RNA in plants.
How to find hairpin loop structure in a large set of long non coding RNA transcripts
bioconductor;rna structure