TPPRED2 is a software package for the prediction of mitochondrial targeting peptides from protein primary sequence.


TPPRED2 is a free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.


TPPRED2 is designed to run on Unix/Linux platforms. The software was written using the Python programming language and it was tested under the Python version 2.7. To let TPpred2 work the following software additional package must be available in your system:

The EMBOSS package can be installed from source code (installation instructions can be found on the package website). In a Debian/Ubuntu Linux distribution (the TPpred2 software was tested under this distribution), the EMBOSS package can be installed through the apt system using a single-line command:

$> sudo apt-get install emboss

Installation and configuration

Once you decided where to keep the software, you must uncompress and untar the package in that location by running the following:

$> tar –xvzf tppred2.tar.gz

This will produce a directory “tppred2”. In order to run tppred2 you need to edit the “bin/” file by setting the TPPRED_ROOT variable to point to the tppred2 installation dir. For example, if tppred2 has been uncompressed into /home/cas/tppred2 you should set:


If you whish, you can copy the 'bin/' script to a directory in the users' path.


The script accepts a single multi-FASTA file in input containing all the sequence the user wants to predict. Run the program as follows:

$> bin/ input_multi_fasta_file.fa

By default the program prints the results to stdout. If you want to redirected the output to file run:

$> bin/ input_multi_fasta_file.fa output_file.txt

The output file looks like the following:

ProteinID                      CleavageSite Score 
sp|P30084|ECHM_HUMAN           27           0.9946
sp|P36957|ODO2_HUMAN           67           0.9693
sp|Q86U06|RBM23_HUMAN          -            0.9996
sp|P38646|GRP75_HUMAN          46           0.9820
sp|P48047|ATPO_HUMAN           24           0.9913
sp|P48201|AT5G3_HUMAN          67           0.8678
sp|P49411|EFTU_HUMAN           43           0.9908
sp|P49448|DHE4_HUMAN           53           0.9782
sp|P55084|ECHB_HUMAN           33           0.9534

For each protein sequence in the input multi-FASTA file the ouptut lists the predicted, the position of the predicted cleavage site (an integer or a "-", in case of non-mitochondrial proteins), and the associated reliability score.