Geneious Biologics (Starter Plan) is a free online analysis tool for annotating and visualizing individual antibody sequences.
This written guide aims at getting you up and running quickly with Geneious Biologics. You can find our series of introductory tutorial videos here, with the first one embedded below. Note that these videos are made for Geneious Biologics Premium, and so include capabilities that aren't available for Starter Plan users.
This guide aims at getting you up and running quickly with Geneious Biologics and includes the following topics:
- Signing In
- Creating a Folder
- Uploading Sequences
- Annotating Sequences
- Viewing and
- Exporting Results
- Contact Us
When you first sign into Geneious Biologics with SSO (Google or Microsoft), the app may take a few moments to create you a new secure account. The app will then take you to your workspace, so that you can get started straight away.
When signing up for the first time using email-based sign in (non SSO), you will need to validate your email address. Simply look for an email from Geneious Biologics, and click the link. You will just need to set a password, and then you can get started with your analyses.
For more details please see our Account Troubleshooting article.
Important: Google Chrome is the browser we test with and officially support. We suggest you use the latest version of Chrome so you will always get the best experience. Some of our users also use the latest version of Microsoft Edge.
Folders and example data
To view analysis examples, click the "Load Sample Data" on the Getting Started page. These examples match the data used in our Sequence Annotation tutorial.
Alternatively, you can create a folder and upload your own sequences. Folders (folder icons on the left side panel) may contain any mixture of documents, such as nucleotide sequences, protein sequences, and sequence lists.
To create your own folder, hover over Workspace, click the menu button (3 vertical dots) and click New folder in the popup menu.
Once you’ve created a folder, you can create more Folders within this folder by hovering your mouse over the folder and clicking the menu button.
Files can be moved from one folder to another using the "Move" icon at the top of the document table.
Folders can also be moved by clicking and dragging them to the desired location.
Importing and uploading files
Once you have created a folder, files can be uploaded using the Upload button or via drag-and-drop.
For more detail about how file upload works and how troubleshoot any issues, see here.
Preprocessing steps are available to prepare sequences for annotation. These steps include: Batch Assembly, Trimming, and Batch Rename. These steps can be used alone or in combination. For an example of how you could use trimming and batch assembly, see our Sequence Annotation tutorial.
Annotating Sequences with the Antibody Annotator
To annotate your sequences, select your uploaded sequences, click the Annotation menu and select Antibody annotator in the dropdown.
Once you have chosen your preferred settings, click Run to start the analysis. You can find out more about the options available here or by clicking the Help button on the bottom right corner of the Antibody annotator popup.
The Antibody Annotator will output a result document with the words Annotated & Clustered appended to the end of your input file name. To view the analysed sequences in a separate tab, select your result document and then click "Pop Out".
For more detail, please see our Antibody Analysis tutorial, which contains a step-by-step walkthrough of analysis using our provided example data.
Viewing Analysis Results
Once the analysis is finished, view your result by selecting the Annotator Result file. To view individual sequences, click the Sequences Table tab and select the reads that you would like to view.
Sequence information such as CDRs, genes, and variants are represented both visually in the viewer, and also as exportable columns in the table above.
You can also group the reads by Heavy or Light V or J Genes. Simply select a gene from the Cluster Table dropdown.
This will show a statistics table with the germline genes that most closely matched your sequences. To see the most common genes, click on the 'Total' column to sort by numberof sequences.
Geneious Biologics also generates a number of graphs which can be useful for Quality Assurance and to discover patterns. An automatically generated selection of graphs can be found in the "Pipeline Report" tab.
Exporting Sequences and Tables
Sequences and Tables can be exported using the 'Export' button above the All Sequences table.
Exports should download automatically once complete, however you can also re-download them in the 'Jobs' table (found in the bottom left corner).
Sequences can be exported in .fasta , .genbank and .geneious format. .geneious is the best choice if you are using Geneious Prime, otherwise we recommend using genbank as this will preserve the sequence annotations.
Tables can be exported as excel or csv format.
Need more help?
There are also many other articles in our extended knowledge base which may be of use, but please note that some of the features mentioned in these articles may only be available in Premium (Growth or Enterprise) plans.