How did Illumina determine the chromosomal location for the potential/putative miRNAs?
To determine the chromosomal location for the potential/putative miRNAs, Illumina used the following procedure: • Select 100% hits (of genome BLAST) for each mature miRNA sequence (if we don’t get 100% match, a value of “zero” is shown in the bgx file) • For each hit select the upstream and downstream pre-miRNA sequence (i.e., 5′-nnn-miRNA-nnnnnnnnnn-3′ and 5′-nnnnnnnnnn-miRNA-nnn-3′) • Generate mfold structures for both upstream and downstream pre-miRNA sequences • Analyze each structure (if the pre-miRNA will fold into the stem-loop structure) • Filter out structures that are below the score threshold (estimated from Sanger training set) • Select the structure with the best score for each blast hit site When multiple 100% hits are found in the genome for one particular mature miRNA sequence, the chromosomal coordinates are listed by the score, i.e., the location with the best score is listed first.
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