Table 3 In silico tools for assessing effects of synonymous variants on miRNA binding
From: In silico methods for predicting functional synonymous variants
Tool | Algorithm/prediction method | Output/score | Year | URL | Ref |
|---|---|---|---|---|---|
TargetScan and Target Scan S | Sequence alignment | Weighted context + + score (from -1 to 1). The scores with a lower negative value indicate a greater prediction of repression | 2005 | ||
MinoTar | Sequence alignment and conservations scoring | Probability | 2010 | [144] | |
Conserved | |||||
Targeting | |||||
miRDB (MirTarget) | Machine Learning (Support vector machine [SVM]) | Target prediction scores between 50 and 100. A predicted target with prediction score > 80 is most likely to be real | 2020 | ||
ComiR | Machine learning (support vector machines) | Ranked vector of scores; therefore, each gene is associated with a reliability of being a target of the set of miRNAs given in input | 2015 (updated in 2020 to include coding regions) | ||
Diana-microT | microT-CDS algorithm | miTG score (from 0 to 1). The closer to 1, the greater the confidence | 2009 (updated in 2013) | https://dianalab.e-ce.uth.gr/html/dianauniverse/index.php?r=microT_CDS | [149] |
Paccmit-CDS | Ranking based on Markov model and sequence alignment | The predictions are ranked according to the P-value that the observed number of conserved and/or accessible seed matches would appear in the target sequence by chance | 2015 | [150] | |
miRanda | Ranking based on seed match, conservation and free energy (G:U pairs allowed in the seed) | mirSVR score (< 0) is an estimate of the miRNA effect on the mRNA expression level. PhastCons score (0–1) measures the conservation of nucleotide positions across multiple vertebrates | 2005 (updated in 2010) | ||
PITA | Ranking based on seed match, free energy, site accessibility and target-site abundance (G:U pairs allowed in the seed) | The predictions are ranked based on having a full match 7- or 8-mer seed and a conservation score of 0.9 or higher | 2007 | https://genie.weizmann.ac.il/pubs/mir07/mir07_prediction.html | [153] |