Welcome to the Monastery,

You've not specified what that query is and whether other technicalities are involved in addition to the syntactic representation and what the comparison contexts that would be addressed are, are you new to Perl and Python or only to BioPerl and BioPython, what do you look for from that comparison? what Perl-specific characteristics you'd wanna check?, you see, There can be a lot of information if you show the right focus...

Here are some starters however,

• BioPython ClustalW
• BioPerl ClustalW

You probably would wanna look at a certain task and then see how BioPerl and BioPython go about achieving it...

I wish you best of luck, I am not being rude as much as I am being only motivational Pubudu and I advice to stick to learning one thing at a time...

Update:Made the links in a list..