I have de novo assembled transcript using Trinity. After annotation with nr database and Coding potential filtering, I have around 10,000 transcripts which can be considered as non-coding transcripts.
From these transcripts, I want to predict how many of these form hairpin loop structure and what miRNA can be generated from these transcripts. I will be thankful for your suggestion.
some people suggest using, RNAfold from the ViennaRNA package and mfold for hairpin loop structure prediction, but I am not sure How these work for large set of transcripts? and further after hairpin loop structure prediction how I can predict the miRNA sequences from all these transcripts.