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];

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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

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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

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In reply to Re: Bioinformatics, Error: explicit package name by Laurent_R
in thread Bioinformatics, Error: explicit package name by mlsmit10

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