example.pl

#!/usr/bin/perl

my $new_seq = Bio::Seq::RichSeq->new();

my $searchio = Bio::SearchIO->new( -format => 'blastxml',
                                   -file   => 'blastout.xml' );
while ( my $result = $searchio->next_result() ) {
    while( my $hit = $result->next_hit ) {
        # process the Bio::Search::Hit::HitI object
        while( my $hsp = $hit->next_hsp ) {
            # process the Bio::Search::HSP::HSPI object

            # tweak the dna seq
            $new_seq->seq( 'AACTGCGCTAGCTACGATCACA' );

            # make a new feature and attach it
            my $feat = Bio::SeqFeature::Generic->new( -start => 5,
                                                      -end   => 523,
                                                      ...
                                                    );
            $new_seq->annotations->add_Annotation($feat);

        }
    }
}