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Misa 05-04-2017 01:09 AM

Identify miRNA in specie not represented in mirBase
Sorry for a dumb question. I have tried search for an answer, but seem to fail on that. What is the general approach for identifying miRNA when you have a bunch of miRNA sequences and a corresponding reference genome for the specie in question, but the specie is not represented in mirBase?

What I have tried is to use miRDeep2 with my sequences aligned to my own species reference genome, but with known mature and hairpin structures from human. I used mature file from mouse and dog as related file. Is this the right way to do it? I get really low alignments for my reads (around 21), is that expected in this case?

I appreciate any thoughts or comments...

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