Contains supplementary methods, one supplementary figure, seven supplementary tables, and supplementary references.

Supplementary Methods. Cost curve calculations; preparations for the two independent test sets, T1 and T2; installation of four miRNA discovery tools and RNAfold; prediction scores of the five tools on T1 and T2. Figure A in S1 File. CROC and CC plots on test datasets T1 and T2. Table A in S1 File. Example of observed labels and predicted scores to make ROC and PRC curves to calculate interpolations. Table B in S1 File. List of 63 papers from PubMed search by “Support Vector Machine AND Genome-wide AND NOT Association”. Table C in S1 File. Descriptions of the three main and 13 sub categories. Table D in S1 File. Three main and 13 sub groups categorize the 58 research papers found by PubMed search. Table E in S1 File. AUC scores of ROC, PRC and CROC from the simulations with random sampling. Table F in S1 File. Five pre-miRNA studies selected from the literature analysis. Table G in S1 File. Seven tools used in the MiRFinder study for the comparisons. Supplementary References. (DOCX)