Hmm, the last time I studied biology and genetics was 40 years ago, not only did I forget most of it, but the knowledge has changed tremendously in the interval. In short, I really don't know much on the subject.

However, I know that the human genome sequencing project has used very widely Perl, thanks in part to the very good tools that have been developed for that, including a number of good reusable modules. I would think that you should take a look at BioPerl and at related Perl modules, it is quite likely that the tools to do what you want already exist and are available on the CPAN or eslewhere.