Is there anyway I can make this run faster?

Don't use a data structure that requires a linear search. Use a hash instead, or, if that would get too large to fit into memory, use an indexed database, e.g. Berkeley DB (you might want to take a look at this recent thread, where a similar problem had been discussed).

If you really need to use an array, search it in a short-circuit way, i.e. don't use grep, but rather a for loop in combination with last, to exit the loop as soon as you've found a match: 

my $found = 0;
for (@A) { if ($_ eq $key) { $found = 1; last } }
if ($found) {
...

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In reply to Re: performance issues with grepping large sorted arrays by almut
in thread performance issues with grepping large sorted arrays by HarshaHegde

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