In silico prediction of precursor microRNA (miRNA), mature miRNA and target genes in rs2149356 sequence

The chromosome 9 GRGh38p12 sequence was downloaded from NCBI accession {"type":"entrez-nucleotide","attrs":{"text":"NC_000009.12","term_id":"568815589","term_text":"NC_000009.12"}}NC_000009.12. The TLR4 gene sequence was identified and used to search for the rs2149356 position. The gene was analyzed using miRNAFold to identify potential microRNA (miRNA) precursor in the comparison between T and G nucleotides [26,27]. Verified feature was 85% and sliding window site was 150 base pairs. To avoid a non-miRNA hairpin-like structure, we also confirmed the result via miRNABoost, in which the delta parameter was 0.25 [28]. The secondary structure was reconstructed by Forna [29]. Consequently, the pre-miRNA sequence identified the miRNA position by ab initio human pre-miRNA and miRNA prediction by hidden Markov model (HMM) algorithms [30]. Finally, the miRNA target analysis was reconstructed from psRNATarget by using Homo sapiens database selection [31]. The target genes of miRNA were functionally annotated via DAVID with high stringent criteria and represented as top sixth enrichment scores [32,33].