in reply to More efficient way to lookup with 2 AoA's.

Use a hash with the gene names as keys. You can then put all the data in one structure,

my %gene = ( gene_name_1 => { start=>'start_1', stop=>'stop_1', chr=>'chr_1'}, # ... );
You could add the score data there, too, unless it's more dynamic than that and is generated elsewhere.

After Compline,
Zaxo