This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Finding Mirna Seed Region By Aligning Mirna And Seeing That Positions 2-8 Hit Fewer Snps

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.

mirna snp sequence
• 4,571 views • link
updated by Biostar Biostar • written by Click downvote Click downvote

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

• 0 views • link
written by Sudeep Sudeep

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.

• 0 views • link
written by Click downvote Click downvote

1 answer

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.

• 0 views • link
written by Click downvote Click downvote

Log in to answer this question.

More posts like this