Geneious Biologics - March 2024

Biologics March 2024 was released on March 25, 2024.

New feature highlights for Geneious Biologics include support for non-antibody therapeutic peptides and the ability to share your analysis options with your team.

Analysis of non-antibody therapeutic peptides and proteins

Peptide Annotator supports analysis of the following data types:

  • Peptide therapeutic sequences (nucleotide or amino acid). For example shorter synthetic sequences with one or more variable loops.
  • Protein therapeutic sequences (nucleotide or amino acid). Typically these are variations of proteins found in vivo, and can be compared against reference sequences. These sequences may get a separate dedicated Annotator in the future - feedback welcome!
  • Any sequence that you might want to cluster, and see liabilities and variants for. Typically these would not be longer than ~400bp.

What does Peptide Annotator do?

  • Cluster your sequences to determine frequency and diversity. Clustering can be amino acid or nucleotide, and may be exact matches or based on sequence similarity
  • Search your sequences for liabilities, which are fully configurable
  • Compares sequences to your custom reference database, identifies the closest match, and annotates any nucleotide or amino acid variants relative to the closest match. This is also useful for identifying the correct translation frame.
  • Add assay data, sort and filter on annotated sequences
  • Align annotated sequences or sequence regions

Learn more about Peptide Annotator.

New Graphs tab

We now display a selection of graphs directly below the Sequences Table. This enables you to get a broad overview of your data while viewing individual sequences. Relevant graphs will also be displayed for any of your specified clusters, when switching between Cluster Tables.

The Graphs tab is next to the Sequence Viewer tab, allowing you to toggle between individual annotated sequences and the graphs.

We now also support adjustable graphs that are populated according to your selection of sequences/cluster rows. You can change what data is being plotted when viewing a cluster by selecting "Full Dataset" "Auto" or "Only selected rows".

Sharing analysis settings

Various operations, including all the Geneious Biologics annotation pipelines (Antibody Annotator, NGS Antibody Annotator and Single Cell Antibody Annotator) allow you to save your settings as Profiles.

This can be useful for saving and re-running tailored settings - for example, Antibody Sequence Liabilities - on different dataset types. Profiles can be set as private to an individual user or shared across an organization.

Learn more about saving your analysis settings as profiles.

Linker databases

A Linker database can be used in addition to either a Germline Gene or Antibody Template database when analyzing bispecific/scFv datasets. Using a linker database will force the boundary FR regions of the two chains on either side of the linker to "snap" to the edges of the defined linker.

If your dataset contains pre-defined linkers between two antibody chains, using a linker database may aid in correctly annotating the boundary regions of the two chains. A linker database can also help you to group your dataset by the linker sequence if you have multiple linkers for screening purposes.

Learn how to make a Linker Database

General analysis workflow improvements

  • Ability to select multiple main reference databases in our annotator. Some examples for this could be:
    • Two different species
    • Multiple different reference scaffolds/templates
    • One of the existing Germline Gene databases with your own custom constant region databases
  • New Clustering options: cluster by number of Amino Acid changes in a sequence region (rather than percentage).
  • Sequence Alignment Improvements:
    • Adding averaged assay data to alignments
    • Ability to color by metadata when viewing a circular sequence alignment

Get started with Geneious today