GREYC BOREA Université de Caen Normandie



PepTraq is an application enabling biologists to explore genomes, transcriptomes, and protein banks easily, by applying filters and transformations, saving searches at any time in fasta format, etc.

PepTraq comes essentially as a desktop application, to be installed on your computer (see below). It can be run on any platform and only requires Java (1.8 or higher) to be installed on your computer, a requirement which is usually already filled.

But PepTraq also comes as a web application designed for users to test its functionalities on reasonably-sized banks, before deciding to install the desktop application. The application is available at

If you have used PepTraq, whether the desktop or the web version, for a published work, please cite:

Bruno Zanuttini, Joël Henry, Christophe Couronne, Abdelkader Ouali, Veronique Robert, et al.. PepTraq: a toolbox for in silico data mining from genome and transcriptome databases. Technical Report, Université de Caen Normandie. 2022.

License and version

PepTraq is distributed under an open source CeCILL-B license. The source code is available below. PepTraq also embeds third-party libraries distributed under an LGPLv2.1 license and an MIT licence (see details below).

The current version is 2.1 (released on April 25, 2022). Release 2.0 had a bug preventing it to run on Windows.


PepTraq is developed at the Université de Caen Normandie, France, in laboratories GREYC (Normandie Université; UNICAEN, CNRS UMR 6072, ENSICAEN) and BOREA (MNHN, CNRS 8067, SU, IRD 207, UCN, UA). It was also supported by a grant by Région Normandie (Projet Émergent n°16E00790/16P03508, 2017-2019).

The web application is hosted by the GREYC laboratory.

If you have technical questions about PepTraq, you want help for installing or using it, or you find a bug, please contact Bruno Zanuttini (

Download and Install

The desktop application can be installed on any computer by following a few easy steps:

  1. make sure you agree with the terms of the CeCILL-B license;
  2. ensure a Java Runtime Environment (JRE), version 1.8 or higher, is installed on your computer; if not, install one (;
  3. determine the command to launch java on your computer; the following assumes it is C:\Program Files\Java\bin\java.exe;
  4. download peptraq-2.1.jar and save it into a folder of your choice on your computer; the following assumes C:\Application\PepTraq 2.1\;
  5. choose the amount of RAM memory to allow to PepTraq, for instance 8 Gigabytes; to choose this, keep in mind that the higher the better, but that you should leave a reasonable amount of memory for the rest of your applications; for instance, if you have 32 Gb available in total, you may want to choose to allow 28 to PepTraq; the following assumes you have chosen 8 Gigabytes, to be written 8g;
  6. create a desktop link (or a script) by setting the following command (the emphasized parts are to be replaced by your own settings):
    "C:\Program Files\Java\bin\java.exe" -Xms8g -Xmx8g -jar "C:\Applications\PepTraq 2.1\peptraq-2.1.jar"
    (double quotes around the Java command and around the path to peptraq-2.1.jar are mandatory as soon as they contain the space character).

Once these steps completed, you can run the application by simply double-clicking your desktop link (or running the script).

Note that if your computer has java installed and is properly configured, you can also directly save peptraq-2.1.jar and double-click it to run it; however, doing so prevents you from increasing the memory allowed to it (the default used by java is typically 256 Mb, which is very low and will not let you explore even middle-sized databases).

Source code

The source code is available (under the CeCILL-B license) over GitLab at If you want to contribute, feel free to ask!

Third-Party Libraries

PepTraq embeds the following libraries :