How to predicate miRNA target without a reference genome

[Mayflower]

Hi, guys

I am trying to predicate miRNA target from a fish species. I have sequenced small RNA and mRNA and then proceed to do the de novo assembly to get the transcriptome. There is no whole genome sequence available for this fish. Any idea about how to predicate the miRNA target without genome sequence and degradome? Thank you so much!

[chhavi.dawar]

Hi
I have recently read about miReader but I havent used it but as much as I have read it works good for non-model organism.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0066857

Hope it helps.

[Mayflower]

Hi,
Thank you so much. I will try and let you know the results.