We obtained a de novo SNV on microRNA coding gene,and genomic data from mirbase told us that this SNV falls in sequence of mature microRNA.However,we failed to tell the altered sequence of this mutated microRNA,nor can we predict alteration of its target genes.One paper(https://www.nature.com/articles/s41380-018-0049-x)mentioned that they achived these goals with miRanda,but miRanda website seems not to be maintained for a long time and has a lot of problems.Is there other methods to adress these two goals(get mutated miRNA sequence&predict its target genes)?Thanks all!
Hi Weichen ,
It the miRNA has being described then searching in a miRNA database as they did in the paper you cited using miRBase, you will be able to get the mature miRNA sequence and introduce the modification. To identify targets take a look at this paper it has a extensive list of resources that may help you Riffo-Campos et al., 2016 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5187787/
And also in tools4miRs, you can find several tools and specifically some methods to evaluate the impact of variations on miRNAs and their targets https://tools4mirs.org/software/mirna_snp_analysis/
Best,
Mar
Hi there
Please check if you find your mutation in some of the databases described in this protocol
http://mirnatools.eu/scenario4.html
If you cannot find it and you are dealing with a new SNP, I am afraid that you should perform a dirty analysis with miRANda or any other basic tool, using the sequence of the miRNA against the given genome. You need to install miRanda in a Linux box, and download your genome to interrogate it.
Best
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