Additional file 12: Figure S6. of Integrated analysis of miRNA and mRNA expression profiles in tilapia gonads at an early stage of sex differentiation TaoWenjing SunLina ShiHongjuan ChengYunying JiangDongneng FuBeide ConteMatthew GammerdingerWilliam KocherThomas WangDeshou 2016 Flowchart depicting the workflow for pre-miRNA prediction. A blastn similarity search of these pre-miRNAs against the tilapia genomic sequences [47] with an E-value cutoff of 0.001. The blastn hits were then manually inspected and compared with their query sequences in order to extract adjacent nucleotides (~30 bp) in both directions that might form part of the pre-miRNA. RNA secondary structure of the cichlid putative miRNA sequences was predicted using Mfold [75] to ensure proper stem–loop folding. A reciprocal blastn of the tilapia pre-miRNAs against known teleost pre-miRNAs was performed to identify the tilapia miRNA and to assign orthology. (TIF 1123 kb)