Table 3.

Summary of the main features, scores and versions of the algorithms included in miRGate

Name	Type	Score	Version	Features
miRanda	Prediction tool	Energy > 140 kcal	3.3a	miRanda uses dynamic programming to score alignments based of the complementarity of nucleotides, allowing G-U wobble pairs.
Pita	Prediction tool	Conservation > 0.5	NA	Identifies initial full complementary seeds for each miRNA in the mRNA and computes the free energy of the unbound and bound double strand. It uses a phylogenetic hidden Markov model (34) called Phastcons; to filter out less conserved predicted target sites.
RNAHybrid	Prediction tool	Score > 0	2.2	Finds energetically most favourable hybridization sites avoiding intramolecular hybridization. Poisson approximation of multiple binding sites and calculation of effective numbers of orthologous targets in comparative studies of multiple organisms are assessed.
microtar	Prediction tool	Energy < 0 Kcal	NA	A program based on mRNA sequence complementarity and RNA duplex energy prediction by using Vienna package, assessing the impact of miRNA binding on complete mRNA molecules.
TargetScan	Prediction tool	Conservation in mammals	6	This algorithm requires perfect seed pairing to score the predictions according the type of the seed match, local AU contribution and mRNA binding site localization.
Tarbase	Validated target database	—	6	Contains detailed information for each miRNA–gene interaction, ranging from miRNA and gene-related facts to information specific to their interaction, including the experimental validation methodologies and their outcomes. All database entries are enriched with function-related data, as well as general information derived from external databases such as UniProt, Ensembl and RefSeq.
miRTarbase	Validated target database	—	4.5	It contains more than 51 000 validated miRNA-gene interactions which are collected by manually surveying pertinent literature retrieved by means of a text mining process aiming at research articles related to functional studies of miRNAs
miRecords	Validated target database	—	—	miRecords hosts a large, high-quality manually curated database of experimentally validated miRNA-target interactions with systematic documentation of experimental support for each interaction using text mining techniques.
OncomirDB	Validated target database	—	—	OncomirDB contains targets that have been validated and published in ∼9000 abstracts. A total number of 2259 manually curated entries with direct experimental evidences were stored.