Table 1.
Tools for predicting animal miRNAs from sRNA-seq data.
| Tool | Algorithm | Mapping tool | Tested in plants | Performance comparison | Validated in wet-lab | Pre-process data | Quantifies expression | Target prediction | User interface |
|---|---|---|---|---|---|---|---|---|---|
| GENERAL TOOLS | |||||||||
| deepBlockAlign | Read block alignment | Not included | Yes | Langenberger et al. (2012), and Pundhir and Gorodkin (2013) | No | No | No | No | Graphics, webserver |
| miRanalyzer | Random forest | Prefix tree | No | Hackenberg et al. (2009) | See below | Partial | Differential expression | MiRanda and TargetScan | Graphics, webserver |
| miRanalyzer (update) | Random forest | Bowtie | Yes | An et al. (2013), Friedländer et al. (2012), Hackenberg et al. (2011) Hansen et al. (2014), Pundhir and Gorodkin (2013), and Williamson et al. (2013) | RT-PCR (Smith et al., 2013), Northern blot (Mayoral et al., 2014) | Yes | Differential expression | TargetSpy | Graphics, webserver, and standalone |
| miRCat | Rules-based | PatMaN | Yes | Moxon et al. (2008) | RT-PCR (Kohli et al., 2014, and Pandey et al., 2014), Northern blot (Donaszi-Ivanov et al., 2013) | Yes | Yes (mirprof), differential expression (colide) | PAREsnip | Graphics, webserver, and standalone |
| miRDeep | Bayesian | Megablast | No | An et al. (2013), Friedländer et al. (2008, 2012), Hendrix et al. (2010), and Williamson et al. (2013) | Northern blot (Friedländer et al., 2008, 2009), RT-PCR (Friedländer et al., 2012) | No | Yes | No | No graphics, standalone |
| miRDeep2 | Bayesian | Bowtie | No | An et al. (2013), Friedländer et al. (2012), Hansen et al. (2014), and Williamson et al. (2013) | Knock-down (Friedländer et al., 2012), RT-PCR (Metpally et al., 2013) | Yes | Yes | No | Graphics, standalone |
| miRDeep* | Bayesian | Bowtie (java version) | No | An et al. (2013), and Hansen et al. (2014) | RT-PCR, knock-down (An et al., 2013) | Yes | Yes | TargetScan | Graphics, standalone (java software) |
| MIReNA | Rules-based | Megablast | Yes | An et al. (2013), Friedländer et al. (2012), and Mathelier and Carbone (2010) | Knock-down (Friedländer et al., 2012) | No | No | No | No graphics |
| miREvo | Bayesian | Bowtie | No | No | No | Yes | Yes | No | Graphics, standalone |
| miRExpress | Sequence homology | Custom mapping tools | No | No | No | Yes | Yes | No | No graphics, standalone |
| miRTRAP | Rules-based | Not included | No | An et al. (2013), Friedländer et al. (2012), and Hendrix et al. (2010) | Knock-down (Friedländer et al., 2012), Northern blot (Hendrix et al., 2010) | No | No | No | No graphics |
| MASSIVELY POOLED DATA | |||||||||
| miRdentify | Feature scoring | Bowtie | No | Hansen et al., 2014 | RT-PCR (Hansen et al., 2014) | Yes | No | No | No graphics |
| PREDICTION WITHOUT REFERENCE GENOME | |||||||||
| MirPlex | Support vector machine | Not included | Yes | Mapleson et al. (2013) | Knock-out (Mapleson et al., 2013) | No | No | No | No graphics |
| MIRPIPE | Sequence homology | BLASTN | No | Kuenne et al. (2014) | No | Yes | Yes | No | Graphics, webserver, and standalone |
Algorithm: the core algorithm for identifying miRNAs. Mapping tool: software used to trace sequenced RNAs to the reference sequences. Tested in plants: if the method has been benchmarked with plant data. Performance comparison: studies that have benchmarked the performance of the tool. Validated in wet-lab: studies that have validated predicted miRNA candidates with experimental methods. Given the overall number of miRNA studies, this list may not be exhaustive. Pre-process data: tools that prepare the FASTQ sequence data for the mapping and prediction steps. Quantifies expression: tools that report estimated miRNA abundances. In addition, some tools report miRNAs that are differentially expressed between samples. Target prediction: tools that predict targets of candidate miRNAs. User interface: tools that have a graphic user interface (as opposed to being operated from the command line). Tools that are run on a webserver (as opposed to being installed and run on a local machine).