New version available
A new version of TPpred (v3) also supporting Chloroplastic targeting signals is available as standalone program at https://github.com/BolognaBiocomp/tppred3.
Introduction
TPPRED2 is a software package for the prediction of mitochondrial targeting peptides from protein primary sequence.
Download
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.
- Source code: tppred2.tar.gz
Requirements
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 hmoment program (EMBOSS version 6.4)
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:
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:
This will produce a directory “tppred2”. In order to run tppred2 you need to edit the “bin/runTPpred2.sh” 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/runTPpred2.sh' script to a directory in the users' path.
Usage
The runTPpred2.sh script accepts a single multi-FASTA file in input containing all the sequence the user wants to predict. Run the program as follows:
By default the program prints the results to stdout. If you want to redirected the output to file run:
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.