From: MTar: a computational microRNA target prediction architecture for human transcriptome
No | Parameter | Parameter Description |
---|---|---|
1 | Seed score | Obtained by the sum of pair scores in the seed region. G:C and A:U with 5, G:U with 2 and the others with -3 |
2 | Out seed score | Obtained by the sum of pair scores in a non-seed region. G:C and A:U with 5, G:U with 2 and the others with -3 |
3 | WC pairs | Number of WC pairs in the duplex |
4 | Wobble pairs | Number of wobble pairs in the duplex |
5 | Mismatches | Number of mismatches in duplex |
6 | Length-bulge | Length of largest bulge in the duplex |
7 | Number-bulges | Number of bulges in the duplex |
8 | Proportion | Proportion of 'A', 'G','C' and 'U' in the target sequence |
9 | Free energy | Free energy is calculated using RNAfold of the target sequence |
10 | Hybridization Energy | Calculated using RNAfold for a duplex formed by the miRNA and its target. RNAfold is the part of ViennaRNA package [39] |
11 | Normalized free energy | NFE = (-1 * free energy of target sequence)/log(length of target * length of miRNA) |
12 | Difference in hybridization energy | Difference in the hybridization energies of miRNA:perfect target (reverse complement of miRNA) duplex and miRNA: target duplex |
13 | Positional pair score | This score is considered by both pairing and positioning. G:C and A:U with 5, G:U with 1, all other mismatches awarded with -3 and the mismatches containing gaps are awarded with -1. Positional weight is 1 for all non-seed position and 2 for all seed position. The total score is obtained by the sum of the product of the weight and the corresponding pair score through out the mirna: target duplex |
14 | Matrix score | Obtained by the sum of diagonal elements in the matrix formed by miRNA and its target. The scores are based on WC pairs: 5, Wobble pairs: 2, Inserts: -1, Deletes: -1, Symmetric mismatches: -3, Mismatches: -2 |
15 | Deviation matrix score | Deviation of the matrix score with the score obtained by a perfect target ie, the reverse complement of miRNA |
16 | Deviation positional score | Deviation of the positional pair score with the score obtained with a perfect target |