This much works on my machine. 
use 5.008;      # Require at least Perl version 5.8
use strict;     # Must declare all variables before using them
use warnings;   # Emit helpful warnings

use Bio::Tools::Analysis::Protein::Mitoprot;

use Bio::PrimarySeq;

my $seq = new Bio::PrimarySeq(
    -seq =>'MIKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL',
    -primary_id=>'test',
); # a Bio::PrimarySeqI object

my $mitoprot = Bio::Tools::Analysis::Protein::Mitoprot->new(-seq => $s
+eq); # sequence must be  >!5aa long and start with an M.

# run Mitoprot prediction on amino acid sequence
$mitoprot->run();

print $mitoprot->result;     # print raw prediction to STDOUT

1;

[download]
It gives the following output: 
Input sequence length : 31 aa


                 VALUES OF COMPUTED PARAMETERS

Net charge of query sequence                    :  +1
Analysed region                                 :  28
Number of basic residues in targeting sequence  :   2
Number of acidic residues in targeting sequence :   1
Cleavage site                                   : not predictable
Cleaved sequence                                : 

                         HYDROPHOBIC SCALE USED

                    GES       KD       GVH1       ECS

H17         :      0.365     1.571    -0.153     0.534
MesoH       :     -0.410    -0.410    -0.410    -0.410
MuHd_075    :     16.751     8.794     5.615     2.837
MuHd_095    :     19.407    14.027     7.300     3.693
MuHd_100    :     14.856    12.028     6.718     2.831
MuHd_105    :     17.763    15.164     7.100     3.885
Hmax_075    :      5.017     5.000    -2.544     3.990
Hmax_095    :      8.313    10.762     0.128     3.806
Hmax_100    :      6.100    10.400     0.010     3.710
Hmax_105    :      4.433     8.400    -2.501     3.640

                            PROBABILITY

of export to mitochondria: 0.0001

In reply to Re: mitoprot bioperl code help by molecules
in thread mitoprot bioperl code help by cburger

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