ImmunExplorer (IMEX)

ImmunExplorer (IMEX) is a software for analyzing IMGT/HighV-QUEST output files and enables a wide range of statistical analyses of clonality and diversity in NGS IG and TR data.


ImmunExplorer (IMEX) uses preprocessed next-generation high-throughput and deep sequencing (NGS) data from human immunoglobulins or antibodies (IG) and T cell receptors (TR) derived from the international ImMunoGeneTics (IMGT®) information system® . IMEX is a user-friendly framework for performing descriptive statistic analyses, clonal expansion and diversity experiments based on the CDR3 sequences and V-(D)-J elements (nucleotide, amino acid level), primer efficiency analyses, and various different visualization experiments based on IMGT® compressed output files.

The software is developed by researchers of the Bioinformatics Research Group at FH OÖ, Hagenberg Campus and researchers of the Immunogenetics Department at the Red Cross Transfusion Center in Linz.


Requirements and Installation of IMEX

IMEX Windows Only:

System requirements: Installation: Be aware that IMEX currently only works with .zip files; but we are working on a new release that also includes performing analyses using *.txz files derived from the IMGT HighV-QUEST information system®.

IMEX Command-line for Windows/Linux/Mac OS X

Please download the latest version for Windows/Linux/Mac OS X: ImmunExplorer v.1.0 beta

Setup and Introduction:


Linux/Mac OS X

How to use IMEX

After starting ImmunExplorer.exe, a startpage offering the following algorithms is shown:

Figure 1: Startscreen of IMEX.
(View > Show Startpage)

Configuration Settings

Two settings have to be configured before IMGT® analyses can be performed properly:

Figure 2: Path configuration window (left) and gene list update window (right).
(Settings > Build IMGT Gene Lists or Settings > Set Output Path)

Preprocessing Methods

The preprocessing methods provided in IMEX enable splitting FASTA (or text) files: Currently the IMGT/HighV-QUEST information system enables the upload of FASTA files containing max. 500,000 sequences. If your file contains more sequences use the Split NGS Data tool of IMEX and prepare the data for the IMGT upload. (Of course you can use the splitter also for FASTA files with less than 500k sequences for your own preprocessing purposes.) After preprocessing the files using IMGT/HighV-QUEST and splitting the original FASTA files, you can use the file merger offered by IMEX. It is important that for all merged parts were created using the same parameter settings having the same filename including the ending "" (e.g., and and so on).

Figure 3: Preprocessing methods: splitter and merger.
(Startpage > Split NGS Data or IMGT Merger; or File > New > IMGT Preprocessing)

Sample Analyses

Single Sample Analysis

You can now load IMGT/HighV-QUEST output files into IMEX and use the following analysis methods:

Figure 4: Single sample analysis: file importer (left) and main workbench for choosing different analysis types.
(View > Startpage > Single Sample Analysis or File > New > Single Sample Analysis)

Figure 5: Clone view (left) and primer view (right).

Multi Sample Analysis

IMEX offers several methods for analysing and comparing samples. By now, descriptive statistics, clone analysis based on the CDR3 sequences, and diversity analysis can be performed automatically. The output files are located on the path you have selected at the beginning.

Comparison Analyses

IMEX offers the following clone comparison methods:

Figure 6: Pairwise clone comparer (CDR3 sequences, AA level). In each input file the top x clones are collected and their frequencies are calculated also for the other input file.
(View > Startpage > Pairwise CDR3 Clone Comparer or File > New > Comparison Analyses > Pairwise CDR3 Clone Comparer)

Figure 7: Multi clone comparer (here shown for V-J clones).
(View > Startpage > Multi Clone Comparer or File > New > Comparison Analyses > Multi Clone Comparer)

All icons used in the software IMEX and icons that are visible on the screenshots are downloaded from IconArchive .



This research project is a collaboration of the Cross Blood Transfusion Service for Upper Austria, Linz and the Bioinformatics Research Group at the University of Applied Sciences Upper Austria, Hagenberg Campus. If there are any questions, problems, ideas please do not hesitate to contact Susanne Schaller, Johannes Weinberger, Martin Danzer or Stephan Winkler.


Relevant Publications


Old releases