ImmunExplorer (IMEX): a software framework for diversity and clonality analyses of immunoglobulins and T cell receptors on the basis of IMGT/HighV-QUEST preprocessed NGS data.
BACKGROUND
Today's modern research of B and T cell antigen receptors (the immunoglobulins (IG) or antibodies and T cell receptors (TR)) forms the basis for detailed analyses of the human adaptive immune system. For instance, insights in the state of the adaptive immune system provide information that is essentially important in monitoring transplantation processes and the regulation of immune suppressiva. In this context, algorithms and tools are necessary for analyzing the IG and TR diversity on nucleotide as well as on amino acid sequence level, identifying highly proliferated clonotypes, determining the diversity of the cell repertoire found in a sample, comparing different states of the human immune system, and visualizing all relevant information.


RESULTS
We here present IMEX, a software framework for the detailed characterization and visualization of the state of human IG and TR repertoires. IMEX offers a broad range of algorithms for statistical analysis of IG and TR data, CDR and V-(D)-J analysis, diversity analysis by calculating the distribution of IG and TR, calculating primer efficiency, and comparing multiple data sets. We use a mathematical model that is able to describe the number of unique clonotypes in a sample taking into account the true number of unique sequences and read errors; we heuristically optimize the parameters of this model. IMEX uses IMGT/HighV-QUEST analysis outputs and includes methods for splitting and merging to enable the submission to this portal and to combine the outputs results, respectively. All calculation results can be visualized and exported.


CONCLUSIONS
IMEX is an user-friendly and flexible framework for performing clonality experiments based on CDR and V-(D)-J rearranged regions, diversity analysis, primer efficiency, and various different visualization experiments. Using IMEX, various immunological reactions and alterations can be investigated in detail. IMEX is freely available for Windows and Unix platforms at http://bioinformatics.fh-hagenberg.at/immunexplorer/.
University of Applied Sciences Upper Austria, Hagenberg Campus, Bioinformatics Research Group, Softwarepark 13, Hagenberg, 4232, Austria. susanne.schaller@fh-hagenberg.at.
Susanne
S
Schaller
Red Cross Transfusion Service of Upper Austria, Krankenhausstrasse 7, Linz, 4020, Austria. johannes.weinberger@o.roteskreuz.at.|Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Donaueschingenstrasse 13, Vienna, 1200, Austria. johannes.weinberger@o.roteskreuz.at.
Johannes
J
Weinberger
Red Cross Transfusion Service of Upper Austria, Krankenhausstrasse 7, Linz, 4020, Austria. raul.jimenezHeredia@o.roteskreuz.at.|Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Donaueschingenstrasse 13, Vienna, 1200, Austria. raul.jimenezHeredia@o.roteskreuz.at.
Raul
R
Jimenez-Heredia
Red Cross Transfusion Service of Upper Austria, Krankenhausstrasse 7, Linz, 4020, Austria. martin.danzer@o.roteskreuz.at.
Martin
M
Danzer
Elisabethinen Hospital, Fadingerstrasse 1, Linz, 4020, Austria. rainer.oberbauer@meduniwien.ac.at.|Medical University of Vienna, Department of Nephrology, Spitalgasse 23, Vienna, 1090, Austria. rainer.oberbauer@meduniwien.ac.at.
Rainer
R
Oberbauer
Red Cross Transfusion Service of Upper Austria, Krankenhausstrasse 7, Linz, 4020, Austria. christian.gabriel@o.roteskreuz.at.
Christian
C
Gabriel
University of Applied Sciences Upper Austria, Hagenberg Campus, Bioinformatics Research Group, Softwarepark 13, Hagenberg, 4232, Austria. stephan.winkler@fh-hagenberg.at.
Stephan M
SM
Winkler
D000465:Algorithms; D004247:DNA / Q000032:analysis* / Q000097:blood; D017931:DNA Primers / Q000235:genetics; D015321:Gene Rearrangement; D006801:Humans; D007136:Immunoglobulins / Q000235:genetics*; D016133:Polymerase Chain Reaction; D011948:Receptors, Antigen, T-Cell / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012984:Software
D017931:DNA Primers; D007136:Immunoglobulins; D011948:Receptors, Antigen, T-Cell; D004247:DNA