miRNA Discovery

[rndouglas]

I may be a bit naive, but I'm trying to see if I can identify miRNA-precursors in a new genome assembly I recently made.

I have available to me:

• de novo assembled genome
• 1x100bp Illumina total RNA RNAseq
• Illumina sRNA RNAseq

Is there any program that can whittle down potential miRNA-precursor loci using all three sets of sequences rather than going through everything by hand?

I suppose in my head I see something like:
map 100bp read to genome --> look for sRNAs that bind within the mapped 100bp potential precursor --> analyze the region to see if it looks decent to actually be a miRNA precursor --> add it to my list to go back and verify experimentally someday.