# Table 1

Parameters used for miRNA target prediction

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

Chandra et al. BMC Bioinformatics 2010 11(Suppl 1):S2   doi:10.1186/1471-2105-11-S1-S2