$ cat splitter.pl 
use strict;
use Data::Dumper;

my $foo=qq(> abcd1234
abcd abcd 
>xyz123 
xyz);
$foo =~ s/\n//g;

my @f = split(/[\>]/,$foo);

$_ = '>' . $_ foreach @f;

print Dumper(\@f);



$ perl splitter.pl
$VAR1 = [
          '>',
          '> abcd1234abcd abcd ',
          '>xyz123 xyz'
        ];