It might be still secret, but there have been reasonably succesful attempts at decoding it. There was a guy called ‘nirved’ who was able to do this, as well as other advanced things, like a new GUI called bex (where is he now?)
There was somebody else who made a perl script from his code called ‘BLASC’, but I don’t think it is still available for download, I can’t find it anymore, I do have the script myself btw
Then there is this C program, which might also help you, but didn’t seem as succesful as the perl script, it crashed often: http://www.scrypt.net/~celer/dnadecoder/