Hi,
Being in bioinformatics myself, I can say that Perl is an excellent choice. To be very honest, I found the Perl Cookbook to be of real assistance, offering the answers 'as you go'. To me it seems learning is more easy that way, because you get the knowledge when you need it. Furthermore, look into the BioPerl project (www.bioperl.org), they have a great big deal of ready-made subroutines, supported by a great number of people around the world.
As an aside, you might also want to dig into the R statistical language, available at cran.r-project.org. There is a project called bioconductor (www.bioconductor.org) also offering loads of packages for dealing with bioinformatics problems.
Bioperl and R run on *NIX as well as windows platforms, although some things just run better on *NIX.
Good luck! Henk van den Toorn
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