FIGURE 9.

SHRiMP mask. Illustration of the set of masks (5 × 20 bases) used for local alignment of the reads against the human miRBase and the human genome by SHRiMP. The symbol 1 indicates positions that must be identical to the corresponding nucleotide in the reference sequence, while the symbol 0 indicates positions that may mismatch (with a penalty to final score). Only reads with perfect alignment of the seed region (location 3–8) and with a maximum of two mismatches in the following bases at any position (location 9–18) were accepted. At the first and last two positions, mismatches were allowed to identify also miRNA length variants. Further selection criteria were adopted at later analysis stages.