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my @filenames;
push @filenames, $_ while (<STDIN>);
...

use Data::Dumper;
print Dumper(@filenames);

ls | my_script.pl

my %hash; # Declare your hash.

$hash{$key} = $sequence; # Assign $sequence to the hash with key $key.

my $sequence_im_looking_for = $hash{$key}; # Get the sequence by looki
+ng it up with its key $key.