I am trying to analyze non-coding RNAs in a newly assembled genome. I had tried Infernal (as reported in published studies), but our collaborator recommended to predict different types of non-coding RNAs (ex. miRNA, tRNA, rRNA) separately using more dedicated tools? For example, predict tRNAs using tRNAscan-SE (which I did and completed), predict miRNAs and rRNAs using BLAST with the respective databases.
I have tried to use BLAST with the miRBase, but I am getting very short alignments and I'm not sure how meaningful it is.
What is the best way to analyze non-coding RNAs in genomic sequence (which I know isn't going to be very accurate anyways)?
Thank you very much!