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 nonseed 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 
Lengthbulge 
Length of largest bulge in the duplex 
7 
Numberbulges 
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 nonseed 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:10.1186/1471210511S1S2 