Hello all!

 I am current analyzing a recently completed reference genome of a non-model organism. This is a stupid question, but I can't seem to find a good answer online: can I identify miRNAs using just genome sequence (the same way that one does ab initio gene prediction)? The whole-genome analysis papers I have found all just said that non-coding RNA were identified by BLAST alignments with databases like Rfam or mirbase, without much more details. A simple alignment seems to not be the answer for so many reasons....

I am super new to genomic analyses... Any help would be greatly appreciated! 

Nancy

Mostly, miRNA's are identified by short-RNA sequencing and then running pipelines like miRDeep. I guess it is possible in principle to blastN all miRbase precursors against your genome, then further check the hits using cmscan against all Rfam. However, this is not a good approach because it will both suffer from large numbers of false positives and low sensitivity.  The question is what you want to do with the predicted miRNAs. If you run target prediction on hypothetical data the result will be totally unreliable, for differential expression analysis, you would need small-RNA seq anyway.

If you want to try how well this works, you could try this pipeline on a well characterized organism:

 - download genome sequence
 - download all miRBase pre-miRNA
 - remove all pre-miRNA that are from this species and keep as test set
 - BlastN all precursors against the genome
 - extract hit sequences 
 - annotate hits using cmscan and keep seqs annotated mi-RNA
 - compare with test set and evaluate the performance  