miRNA binding prediction of SNPs

Question

[Nick]

Looking into effects of SNPs on miRNA-binding. Looking for a tool that allows input of mRNA sequence (not precomputed) and analyzes against miRNA database. Prefer that it takes into consideration a number of factors including but not limited to seed match, conservation, free energy, site accessability, etc... Ultimately want a way to score SNPs comparatively based on their effect on miRNA binding (possibly SNP vs. wild type)...

I've looked into tools like mir-SVR, targetscan, diana-microt, targetminer, comir, PITA, etc. however as far as I can tell, only PITA and miRanda (and ComiR because it uses the others) allows input of mRNA sequence... but I am not sure if these tools are using pre-computed data to match sequence or are computing based on sequence.

Any ideas?

Answer 1

[Nick]

in case anyone is wondering: miRanda and PITA have downloadable source code. miRanda looks primarily at seed match and PITA at effects of secondary structure. I have used publications on variants in 3'UTR miRNA binding regions to validate each tool and found that although results are not identical, both tools produced expected output in top ~10% of score. If you are looking at effect of SNPs on miRNA binding, I would suggest using both tools.