Why not? Perl is capable of doing pretty much anything you can describe clearly how to do.
Do you have a clear-cut method (regardless of language) for doing this? If you can't describe how to do it (regardless of language), you probably can't do it in Perl or any other language.
I suggest you take a look at Algorithm::Diff, which implements the Hunt/McIlroy diff algorithm (which is used by the Unix diff tool). It may give you a way to get started.
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