It would have been nice if you had added [readmore] tags around your rather massive code.

The code looks okay to me. There's nothing, stylistically or logically, that sticks out as bad. (Okay, the die message after open should mention the file name and the error message. File slurping should be a local action.) I also found the code over-commented in places, but that's a matter of taste. However, it could probably make better use of existing modules.

There appears to be a substantial library of genetics-oriented modules on CPAN. I'd look there for useful parts. A module that parses genome/gene information in the PubMed format doesn't seem to be out of the question.

HTML generation is another thing. You could probably use a HTML template, but even plain CGI.pm simplifies HTML generation.

The table you're printing as text output could be nicely done by Text::Table. That would save you the sprintf formats you are using for the table header and content, and their maintenance.

File::Slurp would make file slurping a local action without effect on the rest of the script.

Anno