Precursor identification of mature miRNA
0
2
Entering edit mode
9.0 years ago
Prasad ★ 1.6k

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

mirna precursor • 4.0k views
ADD COMMENT
0
Entering edit mode

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.
ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 2528 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6