The chomp advice above is correct, but for a different approach you could use Damian Conway's IO::Prompt module instead:

use IO::Prompt;

my $query_prompt="$username would like to align your protein sequences
+ globally or locally? (enter either 'g' or 'l')";
my $error_prompt="$username, your selection was incomprehensible (ente
+r either 'g' or 'l'):";

my $alignment_type = prompt ( -prompt => $query_prompt,
                              -require => { $error_prompt => qr/^[gl]$
+/i },
                            );
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