Question: Precursor identification of mature miRNA
2
gravatar for Prasad
4.7 years ago by
Prasad1.6k
India
Prasad1.6k wrote:

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


 

precursor mirna • 2.9k views
ADD COMMENTlink modified 3.3 years ago • written 4.7 years ago by Prasad1.6k

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

Q1) 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. 

Q2) The star strand is mostly complementary to the mature microRNA by may have a few nt overhang.

ADD REPLYlink written 4.7 years ago by mark.ziemann1.2k

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

ADD REPLYlink modified 3.3 years ago • written 4.7 years ago by Prasad1.6k

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.

ADD REPLYlink written 4.6 years ago by mark.ziemann1.2k
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