How do I view and extract annotated sequences?

Viewing annotated sequences

To view individual annotated sequences, select a Biologics Annotator Result document in the Files table. A loading screen with a spinner will appear and upon completion of loading, the sequences will appear.

Note that only the first 5,000 sequences will be shown in the Sequence Table but all the sequences will be selected when Select All is clicked.

Sequences grouping

The NGS result can also be sliced and diced using the Group by operation. For example, if you are interested in looking at the heavy CDR3 region alone, you can group click Group by and select Heavy CDR3 in the dropdown. 

In addition to Grouping, you can also search and filter your NGS result for particular sequences within the entire NGS results or within the Group. To filter within a Group, you have to Group the sequences prior to filtering. Please refer to the following article to learn more about filtering.

These methods of Grouping and Filtering enables you to break down a large body of information into smaller groups allowing the information to be presented in a more useful manner. 

Note that sequence grouping only works with Antibody annotator result sequences.

Extracting annotated sequences

To extract sequences from an NGS result, select the NGS result file, click the Sequences tab in the viewer. Select the sequences that you wish to extract by selecting the checkbox and click Extract.

For the "All Sequences" table, you can choose to either extract each sequence as individual sequences (outputs one document per sequence) or extract all selected sequences into a single sequence list (outputs one document for all sequences).

Click Run to start the sequence extraction operation. This operation will output extracted sequences or sequence list to the same folder where the NGS result file is located.

When you run "Extract" on a row or rows in a Cluster table, it will extract all sequences from that cluster into a list. For example if you extract a row from the Heavy CDR3 table, you will get all sequences in your dataset that contain your selected Heavy CDR3 region.

Saving an image of selected sequences

 You can export a .png image of your sequences, and save it in Geneious Biologics for future reference. The image will contain all of the sequences, not just what is in the viewer. It is recommended that you don't export more than 100 sequences at once.

1. Select your desired sequences in the All Sequences table. 
2. Format your sequences as you want to see them in the image. This could be adjusting to the desired zoom level, choosing annotations to show, and adding any data columns in the "Sidebar" that you would like to display.
3. Click the "Export as Image" button directly above the sequence viewer.
4. Name your image file, and choose whether you would like to automatically download your image. Your image will also be saved in the same Geneious Biologics folder as your original sequences.
   

Downloading Sequences and Tables 

You can also download the analysis tables or the underlying sequences using the Export function. There is more detail about Export here.