Can anybody suggest a software tool that allows for the entry of multiple SNPs and predicts the effect they may have on miRNA?
I have a large number of SNPs so a multiple-entry option is essential. The only appropriate tool I've found is mrSNP but this site has been down for a while now.
Hi Nathaniel,
I have worked with miRNASNP tool (http://www.bioguo.org/miRNASNP/). It is a very good online database because it gives you delta G scores of interaction in wild-type and SNP conditions. However, it does not multiple entry option.
To narrow down your SNP list, I suggest to investigate them in terms of global MAF, since SNPs with very low allele frequency in the population will not be clinically detectable and useful even if that SNP can change the interaction affinity so drastically.
Dear Hossein
Thanks for your response. I am familiar with miRNASNP. The multiple entry remains to be the concern. I have a very diverse population which means global MAFs don't really apply. I need to look at everything and prioritise from there.
Thanks for your input though.
Regards,
Hello Nathaniel
I have worked in "in silico" analysis for the regulation by microRNAs. You can try use this link:
https://bibiserv2.cebitec.uni-bielefeld.de/rnahybrid?id=rnahybrid_view_submission
When you can enter sequences, included your SNPs, of your miRNA and check its effect on target gen. You can check the effect over interaction miRNA-target gene.
Best regards
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