I started out with this code and am not sure if I should add query, BestHit, E-value, and identities as variables before the subroutine.
!/usr/bin/perl-w
use strict;
use warnings;
use BeginPerlBioinfo;
#Declare and initialize variables
my $beginning_annotation='';
my $ending_annotation='';
my %alignments=();
my $alignment='';