brother dep,
Like pmas, I got into bioinformatics "backwards" - from the comp. sci. end of things. It's been a helluva ride so far, and it's only getting better. MadraghRua has got a great list of references for you to start with, but I'd like to add some web-based resources you might find useful:

• Check out the lecture notes for UW's Computational Biology Seminar
• Biomedical Informatics at Stanford
• Introduction to Computational Molecular Biology at WashU

A lot of the bio-related Perl modules are no longer on CPAN - you can find a comprehensive set of bioinformatics tools at http://bioperl.org. On their page, they also provide links to the "other" bio* projects: bioxml, biojava, and biocorba.

Good luck!

- robsv