Use a hash for your smaller array. Something like: 
$, = " ";

# just playing with the =>'s

my @gn_score = (
    [ name_0 => score_0 => ],
    [ name_1 => score_1 => ],
    [ name_2 => score_2 => ],
);

my @gn_start_stop_chr = (
    [ name_0 => b_0 => e_0 => ],
    [ name_1 => b_1 => e_1 => ],
    [ name_2 => b_2 => e_2 => ],
    [ name_0 => b_30 => e_3 => ],
    [ name_2 => b_42=> e_4 => ],
    [ name_1 => b_51=> e_5 => ],
);

my %score;

$score{$_->[0]} = $_->[1] for (@gn_score );

for ( @gn_start_stop_chr) {
    my ( $name => $begin => $end => ) = @$_;
    die unless exists $score{$name};
    print $name,   # or stash your data somewhere
        $score{$name}, $begin, $end, $/;
};

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In reply to Re: More efficient way to lookup with 2 AoA's. by rir
in thread More efficient way to lookup with 2 AoA's. by BioGeek

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