We are nearing the end of the year, and Geneious Biologics has some exciting new features to announce! In this article we will cover the main highlights from the last few months - this includes new visualizations for viewing the relationships across regions and within a specific region or clone (E.g. the Heavy CDR3 or V(D)J). We also now support plotting up to three different assays or other associated data as heatmaps around circular trees. Finally, we have new options for exporting both the aligned sequence and the full parent sequences from alignments.
- Cluster Relationships Visualization
- Cluster Similarity Network and Tree Visualizations
- Assay Data Heatmaps for Circular Trees
- Extended Alignment Flexibility and Sequence Export from Alignments
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Other Improvements
Cluster Relationships Visualization
The Cluster Relationships graph loads automatically below the All Sequences Table upon opening an Annotation Result. This graph shows the the proportion of each identified region/gene which is associated with another region/gene.
The default clusters shown are Heavy V Gene > HCDR3 > VDJ Region. If these clusters do not exist for the result, the first three clustered regions/genes will be displayed. See more here: Using Graphs to interpret Clusters and Clonotypes.
Cluster Similarity Network and Tree Visualizations
These two visualizations are available when switching to the cluster table for a single region, e.g. the Heavy CDR3 Cluster Table. It will display by default the network plot of the clusters for a given region, plotting up to a max of 1000 unique clusters. The tree is also selectable in the graph chooser dropdown.
These tools can help quickly identify the relationships between highly enriched sequences and less common sequences within your dataset. Both the tree and network also enable you to pull out sub-clusters of different lengths. Below is an example of the network plot and tree for the Light CDR3s in our NGS Tutorial 2 pan_1 dataset:
Assay Data Heatmaps for Circular Trees
We now support displaying up to three different heatmap tracks around the outside of an alignment tree. This enables you to tailor what information is displayed alongside the aligned sequences - including any added assay data or other associated information like liability score or number of sequences.
These heatmaps are also available on our Cluster Similarity Tree Plot (above), when using the Cladogram brach transform. To learn more, see our article on Sequence Alignment.
Extended Alignment Flexibility and Sequence Export from Alignments
We have extended the flexibility of what to align and which sequence to select as the representative, particularly from within a cluster table. You can now:
- Choose to align a single representative sequence (by liability score) from within each selected cluster
- In addition, align any region from that representative sequence, even if it is not the current clustered region.
- For example, on the Heavy CDR3 Cluster Table, you can select the top 10 clusters by ID, and align the entire VDJ Region of the representative sequence from within each cluster (by liability score).
When aligning from the All Sequences Table, the representative sequence (by liability score) will automatically be selected for alignment when the option to combine duplicate sequences is turned on.
Export from Alignments
We now support the export of individual selected sequences from within an alignment result. This includes both exporting the aligned region (e.g. the Heavy CDR3) or the parent sequence that Heavy CDR3 came from.
To learn more, see our article on Sequence Alignment.
Other Improvements
- Single Cell Antibody Annotator: Combination clusters like Heavy-Light CDR3 can now be generated. This takes the heavy and light chains that are paired under the same barcode. This is only included in the initial annotation, not add cluster. If you are interested in specific clusters that combine regions from the heavy and light chains, please make sure to include these in your annotation run.
- We have a new curated Human TCR 2024 database released to all customers.
- You can now annotate long read sequences of heavy-light chains which have a bidirectional promotor between the two chains, resulting in opposite-directionality for each chain:
This option is available for both the Antibody Annotator and the NGS Antibody Annotator.