Parameter passing is kind of weird in Perl. When you say SpecifySeqLengths(my $id, my %seq); it's actually creating global variables $id and %seq.
While I agree with the rest of the post and the code example is good, this part is not quite accurate. Those two variables are still lexically scoped to whatever block they're declared in. If that happens to be the scope of the file, one might tend to call them "global", but typically in Perl that term is used for package variables, which are "global" in the sense that they cross the file boundary. There are actually only a limited number of "truly global" variables (i.e. they cross even package boundaries), such as $_ and other special variables (although strangely, that list only seems to be in the Camel's reference section, not in the Perl docs).
