Table 1 Comparison of parameters used in the different miRNA target prediction algorithms
Tool/Parameters | Algorithm | Seed pairing | Target site accessibility | Multiple sites | Conservation filter | Expression profile | Translation inhibition | Availability |
|---|---|---|---|---|---|---|---|---|
Targetfinder | FASTA | + | - | - | - | - | - | Only source code |
TAPIR | FASTA/RNAhybrid | + | + | + | - | - | - | Web server and source code |
Target-align | Smith-Waterman like | - | - | + | - | - | - | Web server and source code |
Target_Prediciton | Scan for matches and RNA hybrid | - | + | - | - | - | - | Only source code |
psRNATarget | Smith-Waterman | - | + | + | - | - | + | Only web server |
p-TAREF | Support Vector Regression (SVR) | - | + | + | - | + | - | Web server and source code |
psRobot | Modified Smith-Waterman | - | - | + | + | + | - | Web server and source code |
miRanda | Local Alignment | + | + | + | - | - | + | Web server and source code |
RNAhybrid | Intramolecular hybridization | + | + | + | - | - | + | Web server and source code |
Targetscan 6.2 (Non- conserved) | Custom made | + | - | + | - | - | + | Only source code |