Currently in so much as I have had a custom services group that codes biological apps in a variety of languages, including Perl.
I work at Invitrogen, mainly the team that has been responsible for Vector NTI (used to be InforMax). I started out with advanced support for enterprise bioinformatics apps, and the job sort of went on from there really. We tend to use C++, Java, Perl, Python - it really depends on what is most convenient.
I have a BSc in Biochemistry, PhD Molecular Neurobiology and have been using Perl and Biology since 1996 or thereabouts.
I suggest enjoying what you're doing while you can. These are good skills to have but supplement with chemoinformatics, ontology or systems biology projects if you can. Just as kits and premade enzymes are tools to be used in the experiments, the language is another means to an end, though a fun and awfully useful one at that.

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