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$ perl -MData::Dumper -e '
@arr = ("A[TCG]GG 3", "CTG[AA] 4");
...
              $st =~ s/\[[ATCG]+\]/S/g; } @arr; 
print Dumper \@nar
'

$VAR1 = [
          'ASGG',
          'CTGS'
        ];