I've been using perl in bioinformatics for 2 years. It's a good language for bioinformatics, for it has well supported biological suite (bioperl) and convenient text parsing. It's good at glue different biological programs together.
Comparing with other languages, it seems that C/C++ don't have a widely accepted "standard" biological suite like bioperl, and you're not likely to cope with seg fault in daily work. So don't use C/C++ unless run-time efficiency is critical. Java is another good choice, because its object system is much stronger than perl, and have Biojava. However, when working with string, I think perl is more convenient. So if you are going to make some large program, you may consider Java.
Python and Ruby may also be good choices, but I don't know much about those languages.
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