Greetings all,
Though this is not really a Perl question per se...( it is Biology related so I'll give it a shot)
I would suggest one method for getting your desired result. You could do this all with HTML styles in a table. This way you could create the graphic for your centromere and telomeres then insert those into the table at the ends or where ever your centromere lies. You could then use the bgcolor attribute of the <td> tag to switch colors based on your criteria (and provide popups for explainations and such if you wanted using JavaScript). This way you are creating the chromosome map with HTML and you don't have to worry about learning GD or Image::Magick to manipulate images, there will only be 3 graphics tops and they will always stay the same. Not to mention if you write this logic well enough perhaps your colleagues might be able to use it to.
Does that make sense?
let me know if you have questions.
-injunjoel