Could anyone please help me in identifying novel miRNAs from plant species without a reference genome?

Question

[anjalinair20]

I am working on MicroRNA seq data analysis. I have completed the preprocessing steps and a blastn search was performed against plant mature MicroRNAs from miRBase to identify conserved miRNAs. It is mentioned in many reference papers that sequences are mapped to a reference genome for novel miRNA prediction. But the whole genome sequence or ESTs of my plant species is not reported. Could any one please help me regarding this?

Answer 1

[andrew.j.skelton73]

As hacky as this sounds, if you're looking at it from a purely investigative perspective you could do the following:

Download a closely related species from miRBase (hairpin and mature sequences) - This will be your reference, as miRNAs are generally pretty well conserved.

Run miRDeep2 with the above as your reference, and grab some other closely related ones as it'll be required as a parameter.

miRDeep2 is run on a per sample basis, not a whole experiment, so you're limited to your individual samples.

Answer 2

[Mohammad Reza Bakhtiarizadeh]

Hi

You can try these software:

• MIRPIPE
• miReader
• MirPlex