Finding Mirna Seed Region By Aligning Mirna And Seeing That Positions 2-8 Hit Fewer Snps

Question

[Click downvote]

I think the following method has been used to find seed sequences in miRNA:

align miRNA against the relevant places in the genome, count how many times each miRNA hits a SNP and then see that region 2-8 of the miRNA hits fewer SNPs than the rest. Voila, seed sequence inferred at position 2-8.

Does anybody recognize this or a similar method? If so I'd like the name and relevant paper please.

[Sudeep]

Could you add some info on your source for miRNA sequences ? is it from RNA-seq, databases or "miRNAs of interest" from publications ?

[Click downvote]

I have no source for miRNA- I've used the technique on a different type of RNA, but want to cite those that invented the method.

[Jeremy Leipzig]

for plants or animals?

Answer 1

[Click downvote]

Found one that seems to use the technique: http://www.nature.com/ng/journal/v38/n12/full/ng1910.html (fig 1. illustrates it)

But if anyone else find any others I'll upvote and accept that as the answer.