AptaAnalyzer™-SELEX

The innovative and user-friendly sequencing software tool AptaAnalyzerTM-SELEX exploits next-generation sequencing analysis to leverage and streamline the lead discovery process of in vitro or in vivo aptamer selection experiments. The target addressing aptamer scaffolds can be constrained and contain several random and constant parts “displaying” stretches of nucleotides in a more structured fashion. Our sequence analysis software makes it now very easy to digitalize SELEX experiments. It enables intuitive parsing of raw sequence datasets corresponding to initial libraries or advanced selection rounds, individual as well as comparative analysis of selection rounds, clear-cut presentation of results in the form of tables and graphs, structuring data in projects and subprojects, and archiving them in databases.

Archiving and structuring of SELEX experiments

AptaAnalyzer™-SELEX 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 generation of results in form of table views and publication level graphics.

Experiments are organized in a database within projects and subprojects.

The “Sequence Parts Editor” enables the definition of the aptamer with its constant (dark grey) and variable (light grey) regions. Also complex molecules with several constant and variable part can be easily defined.

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

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

Table views

Overview on the level of clones with AptaAnalyzer™-SELEX: Full sequences are listed, whereby customer defined constant and variable regions are listed in separate columns.

Tables for each of the variable regions are given which provide interlinked information on two level of details. The table on the top shows “leader sequences” each representing a family. The table in the middle gives sequences of all family members of a selected sequence.

List of identified clones can be further expanded by user defined columns, for example: Experimental data like binding constants, specificity scores or virtual any other clone specific information can be included and stored in the database.

Custom defined table filters can be applied to view only clones matching defined criteria. Also user-defined columns, e.g. “Specificity” or “Affinity” can be used as filtering criteria.

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

Excel can be used to add columns with additional data. The reimport of edited tables updates the database with such sequence information, e.g. wet lab data like “Specificity or Affinity”.

Graphs for single dataset analysis

Bar charts visualize frequency of defined sequence regions (here of variable region od SELEX round 7).

Bar charts visualize the random region length distribution (here of SELEX round 7).

Stacked bar chart diagrams show the distribution of nucleotides of variable regions, e.g. to asses the quality of starting libraries or to identify conserved and variable sequence parts of defined populations (here of a defined family).

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 to track the frequency of sequences over multiple experiments, e.g. selection rounds.

Graphs give information on several levels of detail: A click on a defined bar chart series of a “family” visualizes the frequency of its respective family members (blue framed).

Scatter plots enable to compare the frequency distribution of complete clones or defined sequence regions of two experiments, e.g. selection rounds.

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

Exact sequences are obtained via csv-export.

Venn diagrams enable to identify sequences that occur in defined experiments.

A click on respective segments (here yellow) extracts all sequences that are part of A (round 5) and B (panning round 6)  but not of experiment C (variant of panning round 6).

We designed AptaAnalyzerTMSELEX 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 AptaAnalyzerTM-SELEX and profit from:

  • Optimization of your selection platform by opening the black box of SELEX experiments
  • Quality control of synthetic starting libraries enhancing SELEX screening techniques
  • Sequence analysis of single or multiple oligonucleotide inserts
  • Accelerated and advanced identification even of rare ligands by intelligent clustering of ligand families
  • Direct linkage of sequence information with wet-lab data like affinity or specificity, which can be implemented into the database
  • Improved optimization of lead compounds
  • Improved patenting strategies by profound sequence analysis information

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.

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