Over the past few months we have been working on some exciting new features for Geneious Biologics. This article covers some of the latest highlights, such as manual sequence editing, dual nanobody (VHH-VHH) support, and protein scaffold reference databases.
- Manual Sequence Editing
- NGS Antibody Annotator
- Enrichment and Alignment Visualisations
- VHH and Dual Nanobody Analysis
- Reference Database Creator
- General Analysis Workflow Improvements
- Coming Soon
Sequence Editing
Sequence editing is now live in Geneious Biologics! This first release is primarily targeted around enabling QA workflows, allowing you to perform manual base correction before your final annotation and analysis.
Currently sequence editing is supported in sequences and sequence lists of less that 1000 sequences. For editing from Annotator Results, you can extract your chosen sequences into a separate list first.
See Editing your Sequences to learn more, or Sequence Repair if you are interested in an automated option.
Note: This is a early release feature - we would love to hear any feedback about what you would like to see next, particularly around Humanisation and other sequence engineering applications!
NGS Antibody Annotator
Our new annotation pipeline NGS Antibody Annotator is ideal for working with large NGS datasets (e.g. millions of sequences).
Unlike Antibody Annotator, the central view shows unique clones present, with poor quality sequences automatically filtered out.
IMPORTANT NOTE: To ensure optimal performance, Antibody Annotator will no longer be available as an option for datasets of 20 million sequences or more. For these datasets users can choose between NGS Antibody Annotator, and Single Cell Antibody Annotator. Please contact support if you have any questions.
Enrichment and Alignment Visualisations
- Tracking clonal enrichment over panning rounds with a flexible scatter plot generator.
- See our Comparing Results across experiments article.
- See our Comparing Results across experiments article.
- New Circular view for Sequence Alignments.
VHH and Dual Nanobody Analysis
Dual nanobody (VHH-VHH) analysis is now supported in Antibody Annotator and NGS Antibody Annotator.
This can be combined with our new Template reference databases to annotate your sequences from known variable region scaffolds. Alternatively, we also have a new Alpaca IgG gene reference database available as a zero set-up option.
Reference Database Creation Wizard
Our new database creation wizard helps automatically format genes and variable regions, making adding reference databases for new projects quick and easy. See How to make a Custom Reference Database for more details.
General Analysis Workflow Improvements
- Ability to enumerate pairings between multiple associated chains using a Name Scheme when running Antibody Annotator.
- For example: pairing a heavy chain with both a kappa and lambda chain, or multiple heavy-light chain combinations in pre-analysed Single Cell data.
- For example: pairing a heavy chain with both a kappa and lambda chain, or multiple heavy-light chain combinations in pre-analysed Single Cell data.
- Ability to add clusters within an Annotation result: new Add Clusters pipeline.
Note: This replaces the old Recluster pipeline, which is no longer available. - New 'Antibody Template' reference database type, which provides full support for using VDJ/VJ sequence scaffolds as your reference database sequences (instead of germline genes).
- Support for using protein sequences in an Antibody Template reference database.
- Updated Camelid (Alpaca) IgG Reference database is now available.
- Newick format export of alignment trees.
- Import of Excel files as table documents, which can be viewed and added to annotation results.
- New streamlined layout for the options of Antibody Annotator and Single Clone Analysis.
Other
- New version of the Geneious Biologics Prime integration is available:
Using Geneious Prime together with Geneious Biologics.
- New Discovery video series:
Explore Antibody Discovery | Geneious Academy.
Coming Soon
- Analysis of non-antibody therapeutic peptides and proteins
- Further improvements for VHH-VHH and similar multispecific analyses
- New clustering visualisations, and alignment improvements
- Ability to save and share job/pipeline options
If you have any questions or feedback, please contact us!