alicia:
It's just possible that some of us are unfamiliar with BIAST, BESTHIT, E-Value and uncertain precisely what "the identies" means in this context. Oh, /me fits that category. It's also possible someone else is expert on all the named whatcha'ma'call'its, and thus able to provide assistance without you supplying the prerequisites for a good question here.

But it's a good idea to satisfy those anyway. They can be found at On asking for help and How do I post a question effectively?. Briefly, they include the code you've written, a data sample, and an unambiguous explanation of why your results don't satisfy you.

Your SoPW doesn't tell us whether you know how to open and read a file(s?); how to assign content to variables; or how to write a regex. For the first, see perldoc open and any number of nodes here dealing with read, while, <> which can be found using Super Search. Generally, that same Super Search will offer examples of assignments to $vars. And for regex help, start with perldoc perlre and perldoc perlretut and the splendid tuts here at the Monastery.

The fact you found BioPerl is commendable, but you're going to need to do more than that.. and, in any case, your statement that you "need to do the question without BioPerl" raises other questions; first, "Is this homework or the like?" and second, "Why?"