I am doing a next gen sequencing project to identify miRNA in brassica. I made the small RNA libraries and sent them for sequencing and subsequent analysis. The data that I got back shows a lot of novel miRNAs and also some novel miRNAs with similarity to already known miRNAs in miRbase. For eg. aaaacggaaucguaagcuuc is called siimilar to osa-miR2121a (whose sequence is aaaacggagcgguccauuagcgcg). The similarity between these two miRNAs is between 2-8nt. Same criteria is for other miRNAs.
My question is how should I interpret this data? When doing clustering of miRNAs in families which sequence should I use? I think similarity at seed region can not be used as a criteria for clustering!
I would welcome any kind of suggestions.