Is there any tool that provide to find miRNA from motif sequences?

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Luis A. Arteaga-Figueroa

I think you could use MEME for clustering methylated motifs (in case you'ven't done it) and then use miRanda (http://www.mirtoolsgallery.org/miRToolsGallery/node/1055) to check if that motifs are known targets of miRNA.

Azime Akçaöz

Thank you for your answers. I will try it.