iso-miRNA targeted mRNA

Question

[ti&te]

Dear all,

we did small RNA sequencing and now we are analysisng our data. Does anyone know any tool, script or software for iso-miRNA - Gene(mRNA) target prediction? I know that for mature miRNAs there are mirWalk, mirDB and other, but I don't find it for isoforms....

Thank you for your help...

Answer 1

[Lars Juhl Jensen]

Considering that the functional entity that targets other genes is the mature miRNA and that iso-miRNAs give rise to identical mature miRNAs, I cannot see how you would define different targets for them. In my opinion, the sensible way to perform the analysis is to predict targets for the mature miRNAs and, if necessary, assign all iso-miRNAs with the targets of their respective mature miRNA.