How to predict the interactions between SAGs and miRNAs?

Each plant miRNA typically contains a single sequence motif with near-perfect complementarity to its target. According to the RNAhybrid method [1], the criteria we selected to predict interaction between SAGs and miRNAs are mentioned below:

1. Perfect base pairing of the duplex from nucleotide 8 to 12 counting from the 5' end of the miRNA is needed, because this region includs the presumptive cleavage site in the target sequence
2. Loops or bulges are no morn than 1 nucleotide in either strand
3. The end overhangs with a maximum length of 1 nucleotide in either strand
4. The minimum free energy (MFE) value is required to be 60% of the MFE calculated for a miRNA:mRNA hybrid perfect match
5. For each target sequence, only the best target site for a miRNA is given

For each miRNA and SAG interaction, the details includes miRNA name, target gene name, MFE, P-value, and interactive position. The cross links of miRNAs to miRBase [2] are also given.

Note: The mRNA sequence of each SAG is used to predict the interaction with miRNA.


[1] Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R: Fast and effective prediction of microRNA/target duplexes. RNA. 2004 10:1507-1517.
[2] Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ: miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008 36(Database issue):D154-158.

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