Second, TargetScan (http://www.targetscan.org) was used to detect target gene candidates based on seed complementarity on UTR database 6.0 and our porcine RefSeq transcript with our miRNA seed sequence [ 99].
Therefore, numerous miRNA target prediction methods have been proposed such as miRanda [ 22], TargetScan(S) [ 23], RNA22 [ 24], Diana-MicroT [ 25], PicTar [ 26], RNAhybrid [ 27], and miTarget [ 28], based on seed complementarity, thermodynamics, conservation, Bayesian statistics, SVM, HMM, artificial neural networks, etc.
Furthermore, the ability of miRNAs to target mRNAs with only partial complementarity [ 12] indicates that in many cases identification of miRNA targets may not be possible based on seed match complementarity alone [ 10].
The mature miRNA with RISC will bind to and silence its target mRNA based on seed sequence complementarity, generally at the 3' UTR.
During recent years, a number of prediction algorithms have been developed to track miRNA targeting based on seed pairing, overall complementarity, pairing stability, target site evolutionary conservation and UTR context.
To this end, a number of predictive tools, namely, TargetScan, 9, 10 PicTar, 11 miRanda, 12, 13 and PITA, 14 are used to identify the MMIs based on the seed complementarity between miRNAs and the 3′UTRs of specific mRNAs.
miRNAs are commonly grouped into families, the members of which share the same seed and are thus predicted to target the same genes by algorithms relying on seed complementarity only.
miRcode identifies putative target sites based on established principles: seed complementarity and evolutionary conservation (see Supplementary Material for detailed methods).
Although miRNAs recognize their target genes based on the complementarity to the seed region, our results suggested that miRNAs with the same seed sequences but different duplex structures may have different silencing efficacies according to the Tm2 8 − 0.53 × miTm1 5 values.
Some authors [ 10, 20] suggest a traditional miRNA-like silencing based on complementarity of the 5' seed sequence of a tRF to a short sub-sequence within a 3' UTR of a transcript [ 16– 16].
