That's better, but it would be even better if posted code that was self contained. Also, as many will mention, always use strict; and use warnings; unless you have a specific reason you're not. I know you're using them, but you should show us you're using them.

The main problem I'm seeing in your script is that you're pushing a list into an array. Your description implies you want a matrix. In order to do that, you'll have to push an array reference into your @genome array:

Perl only stores scalars in arrays and hash values, so, in order to create a multi-level datastructure, you need fill the array with a reference to the array.

A minor thing is that you'll probably miss your last chromosome because of how you're parsing the file. After you hit the end of the file, and there isn't a dangling header, you'll still have a lot of data in $temp_str that doesn't make it into @genome.

Edit: also, as toolic says, you should change you split line to: