PepTraq

Presentation

PepTraq is an application allowing 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. 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.

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 (2017-2019).

Information and Contact

If you have technical questions about PepTraq, you want help for installing or using it, or you find a bug, please contact Bruno Zanuttini (bruno.zanuttini@unicaen.fr).

If you need any help while using PepTraq to understand the different features, please contact Céline Gaudin-Zatylny (celine.gaudin@unicaen.fr) or Joël Henry (joel.henry@unicaen.fr).

Installation

The desktop application can be installed on any computer by following a few easy steps (the third-party libraries to be installed are explained at the end of this section):

  1. ensure a Java Runtime Environment (JRE), version 1.8 or higher, is installed on your computer; if not, install one (https://www.oracle.com/fr/java/technologies/javase-downloads.html);
  2. download peptraq.jar and save it into a folder of your choice on your computer,
  3. download the other required archives and save them into the same folder under the names given below:
  4. create a desktop link (or a script) by setting the following command:
    java -XmsAAAA -XmxAAAA -jar /path/to/peptraq1.0.jar
    where "AAAA" stands for the RAM memory which you want to allow to PepTraq; of course, the more the better, but this depends on your computer/server; for instance, if you want to allow 1 gigabyte and have saved the file in "C:\Directory 1\PepTraq", set the command
    java -Xms1g -Xmx1g -jar "C:\Directory 1\PepTraq\peptraq1.0.jar"
    Replace "1g" by "300m" or by "16g" if you want to allow 300 megabytes or 16 gigabytes instead of 1 gigabyte.

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

Third-Party Libraries

Versions and History

The current version is 1.0, made available on May 9, 2021.