Hi,
I'm trying to generate a reference table of positions in Alu sequences according to the Ancestral Alu sequence. In order to do so, I am using the Alu alignments provided by Repbase and mapping each position of the genome to the correspondent position within a specific Alu subfamily. The next step would be to map the Alu subfamily position to the Ancestral reference. I was thinking in using the subfamily alignment provided by Repbase: http://www.repeatmasker.org/AluSubfamilies/humanAluSubfamilies.html, however, I noticed that the newest Alu subfamilies (AluYh3, AluYh3a3, AluYh7, AluYj4, AluYk2, AluYk3, AluYm1) are not included. I thought in searching for the subfamily reference sequences in Repbase (https://www.girinst.org/repbase/update/browse.php?letter=A&division=Homo+sapiens&customdivision=&rank=&type=SINE&autonomous=1&nonautonomous=1&simple=1&format=FASTA#browse) and then make my own alignment to the ancestral sequence, but I coudn't find those subfamilies. I have also checked for the source answered in this previous post: Reference Alignments For Human Alu Families Or Subfamilies? but it is quite outdated. My question is, is there any source where I can get an Alu subfamilies alignment? or where could I find the reference sequence for the newest Alu families?
Thanks,
