in reply to Other Bioinformatics Monks Out There?
I use Perl on a daily basis to hack out scripts and to quickly ask questions about the datasets that I deal with. BioPerl is central to a lot of the work that I'm doing, as it makes tying a lot of Perl programs together very easy. However, every now and then I find it a bit lacking. For example, I'm currently doing a bit of work on RNA editing and trans-splicing, and I'm writing some custom objects that trans-splice and assemble sequences from trans-spliced FeatureTable definitions.
I'm also employed as a sysadmin, and I find Perl invaluable for writing Nagios plugins, database updating scripts and testing suites for various services. Perl is just a good way to get all sorts of computer-related things done.