*2.2.3. Determination of hairpin conservation of Novel MicroRNAs*

We classified all the candidate miRNAs using the PhastCon database at the University of California at Santa Cruz.**(10, 11)** This database has scores for each nucleotide in the human genome relative to its degree of conservation when compared to nucleotides in the armadillo, bush baby, cat, chicken, chimpanzee, cow, dog, elephant, frog, fugu, guinea pig, hedgehog, horse, lizard, medaka, mouse, opossum, platypus, rabbit, rat, rhesus monkey, shrew, stickleback, tenrec, tetraodon, tree shrew, and zebrafish. The algorithm is based on a phylogenetic hidden Markov model that uses best-in-genome pairwise alignment for each species (based on BLASTZ), followed by multiple alignment of the twenty eight genomes. A hairpin was defined as conserved if the average PhastCon conservation score over the 28 species for any 15-nt sequence in the hairpin stem was at least 0.8 .**(12)**
