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Table 1 Comparison of parameters used in the different miRNA target prediction algorithms

From: A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction

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
  1. ‘+’ Represent feature used, ‘-‘ indicates that these features were not used.