You'd think being a recent computer science graduate would leave me a little more clued up!
No, I'd think it would leave you knowing how to do nothing but write Java programs on Windows. *rimshot*
Snarkiness about the state of CS education aside, it's hard to go wrong with The Llama (Learning Perl) for getting started. Conway's OO Perl book is an excellent resource for getting a good solid grip on that side of things once you're ready. There's actually a book titled Beginning Perl for Bioinformatics, but I haven't read it (and I don't work in the field), so all I can say about it is that you might want to find a copy and scope it out.
Once you get going, the contents of perldoc (especially perldoc -f) will likely become your primary reference source.