Precursor identification of mature miRNA

Question

[Prasad]

Hi,

I have set of mature miRNA sequences (18-36 bp range) [genome sequence is not available]. For these mature mirna sequences I want to find exact precursor sequences. I aligned mature sequence to genome and took upstream and downstream 50 bp including mature mirna and did the rna folding but I am getting structure for full. my questions are

1. How do I predict exact precursor sequence
2. To identify miRNA* for existing mature rna. Should I just reverse complement the mature mirna?

Any suggestions are appreciated. Thanks

[mark.ziemann]

Prasad, Which species are you looking at? Do you have some microRNA-seq data already?

1. There are lots of different software for hairpin microRNA precursor prediction but they work better with some microRNA-seq data as well; consider miR-Deep2 and miReap as two options.
2. The star strand is mostly complementary to the mature microRNA by may have a few nt overhang.

[Prasad]

Thanks for the reply. i am working on plant species with no genome. I want to predict precursor sequence for each of mirna. i will try with mir-Deep2

[mark.ziemann]

Do you have small RNA seq data to help you identify the miR genes? Because miR-Deep2 is limited to a few animal species only, miR-Deep-P might be more appropriate.