my $sequence_to_parse =">test\nATG\nGGG";
while ( $sequence_to_parse =~ m/(^>.+)|(^.+)/gm ) {
    if ( defined $1 ) {
        print "got first line \$1 ($1)\n";
    }
    elsif ( defined $2 ) {
        print "got other line \$2 ($2)\n";
    }
    else {
        print "UH OH \n";
    }
}
__END__
got first line $1 (>test)
got other line $2 (ATG)
got other line $2 (GGG)