What is the purpose of having reference genome of other species during miRDeep2?

Question

[nivya.james2016]

Hi all,

I am doing miRNA Seq analysis and I am new to it. I have indexed my genome using bowtie and mapped it. Inorder to identify the known or novel miRNAs, I thought of using miRDeep2 tool.

I read a protocol saying you need mature miRNA of closely related species (eg: Gorilla) for carrying out miRDeep2 tool.

What is the purpose of having mature miRNA of other species and also genome and mature miRNA of species interested??

Thank you in advance.

[Buffo]

Probably because most of the mature miRNAs described to date, are conserved sequences. One condition to filter probable miRNAs to other short non-codings RNAs is if they (or closely related short sequences) have been described to show some inhibitor activity.