Table 1. The performance comparison between release 2017 and release 2011 using default scoring schema and 147 validated miRNA–mRNA interactions in our Arabidopsis benchmark dataset.

	Recalled interactions	Recall rate (%)	Total predictions in the output
2011 Release, Schema V1	134	91.1	9,204
2017 Release, Schema V2	143	97.3	9,654

*The comparison was performed between 65 unique miRNAs/ta-siRNAs in the benchmark dataset (Supplementary Table S1) and the Arabidopsis TAIR10 transcripts. Maximum expectation was set to 5.0 and the maximum number of allowed top targets for each miRNA was set to 200 for both scoring schemas.