Identifying Olive Baboon Alu Insertions

Loci were ascertained by first using RepeatMasker [47 ] on the reference genome of the olive baboon, Papio anubis (Panu_2.0). Alu elements were parsed out of the resulting RepeatMasker file. The sequence of each full length (starts at or before position 4 in the element and ends after position 266) AluY insertion, along with 500 bases of flanking in 5′ and 3′ direction of the Alu element, was compared to the rhesus macaque (rheMac8) and human (hg19) reference genomes using BLAT [48 (link)]. We then compared the resulting BLAT files for any locus that had an appropriate gap size in the genomes that would indicate an insertion that was only present in the genome of the olive baboon.