Yes, the missing semi-colon is the cause for the errors displayed on your screen, but the most important issue is that this line:

my @third_fragments = grep -v ($rsite3), $second_fragments[$i];
[download]

is just plain wrong Perl syntax (even with the added semi-colon). Perl's grep has little to do with the Unix shell grep (at least as far as syntax is concerned). The "-v" flag does not exist in Perl for the grep function. Please try:

perldoc -f grep
[download]

Just a quick example on how to use grep in Perl:

$ perl -e 'my @number_larger_than_5 = grep {$_ > 5} 1..10; print " @nu
+mber_larger_than_5";'
 6 7 8 9 10
[download]