AptaAnalyzer™-TCR: A sequence analysis software tool for TCR profiling

The innovative and user-friendly sequencing software tool AptaAnalyzerTM-TCR exploits next-generation sequencing analysis to leverage and streamline the analysis of T-cell receptors (TCRs). Your research will profit from the integration of next-generation sequence analysis to analyze the status of the immune system by profiling its T-cell receptor repertoire. Our sequence analysis software makes it now very easy to analyze the digitalized immune system of individuals (human, mouse) by intuitive parsing of raw sequence datasets. Sequence analysis of datasets corresponding to defined time points in the response of the immune system is possible individually as well as comparably at very high resolution with our software AptaAnalyzerTM-TCR. You profit from clear-cut presentation of results in the form of tables and graphs, the structuring of data in projects and subprojects, and archiving projects and subprojects in databases.

Archiving and structuring of the TCR immune status

AptaAnalyzer™-TCR supports the complete workflow in a very intuitive way. It is one tool for parsing of raw data, archiving of datasets, analysis of experiments and for generation of results in form of table views and publication level graphics.

Experiments are organized in a database within projects and subprojects.

The graphical parser” enables an almost parameter free reading of alpha and beta chains from human or mouse.

Quick and easy NGS data interpretation and easy generation of publication level material enables to exploit NGS data for actual experiments.

Publication level graphs can be configured and its data values can be exported into Excel.

Table views

AptaAnalyzer™-TCR shows results on the level of clones. Full sequences are listed in separate columns.

Tables (filtered or unfiltered) can be exported as csv-files for comfortable data transfer into Excel or other third party software.

Three tables for each of the variable regions (here for a CDR3 region) are shown, which provide information on three level of details. The table on the top shows “leader sequences” each representing a family. The table in the middle indicates sequences of all family members of selected family and table on the bottom shows the selected clone on the DNA-level. Information and table views are interlinked and change with the selected region.

Custom defined table filters can be applied to view only clones that match defined criteria.

Graphs for single dataset analysis

Bar charts visualize frequency of defined sequence regions. Region of a human alpha-CDR3 region is depicted here.

Bar charts visualize distribution of length. Shown is a human CDR3 (alpha chain). The Gaussian like distribution reflects an unbiased immune system at day 0.

A heat map visualizes frequent combinations of dominant CDR3s with V-genes.

Highly frequent combinations (red and yellow) are marked according to the colour ramp.

Stacked bar chart diagrams show the distribution of amino acids of CDR regions, for example to identify conserved and variable sequence parts of defined populations.

The data values of graphs can be exported to be further processed in Excel or other third party software.

Graphs for comparative dataset analysis

Bar chart series enable for example to track the frequency of CDR3 sequences over multiple experiments (e.g. different individuals and/or time points).

Graphs show information on several levels of detail. A click on a defined bar chart series of a family (leader sequence) visualizes the frequency of its respective family members (blue framed).

Scatter plots enable to compare the frequency distribution of two experiments, e.g. (stimulated vs. unstimulated).

Graphs give information on several levels of detail. A click on a defined dot of a “CDR3 family” visualizes the frequency distribution of its respective family members (blue framed).

Venn diagrams enable to identify TCRs (or its CDR3s), which occur in defined experiments.

A click on a respective segment (here orange) extracts all sequences that are part of positive experiments A and B but not of control experiments C and D.

We designed AptaAnalyzerTM-TCR as an easy-to-use sequence analysis software, which provides a maximum flexibility in creating and storing analysis results in figures and tables. You can digitalize any NGS or Sanger sequence data sets provided in FASTA/FASTQ format.

Get started with the analysis of your sequences with es AptaAnalyzerTM-TCR and profit from:

  • Comprehensive comparability of the TCR status of all individuals/time points you ever parsed into your database
  • Sequence analysis of V-, CDR-  or J-Regions of TCR alpha and beta chains
  • Accelerated and advanced identification even of rare TCRs by intelligent clustering of receptor families as well as by digital spectratyping
  • Annotation of V- and J-region annotation according to IMGT-standard.

AptaIT offers very flexible arrangements either as Pay-per-Use stick (dongle) with a predefined number of datasets (10, 50, 100, 250, 500) or annual license arrangements for unlimited use.

Please contact us for further information.