This article outlines how to edit your annotated sequences. Editing includes deleting, replacing or inserting residues or bases. It does not currently include adding custom annotations. If you are interested in annotating your sequences with non IgG-like regions, please see our Using Feature Databases article.
- Extracting sequences from a result to edit
- Editing options
- Strategies for editing to improve developability
Extracting sequences from a result to edit
Annotated sequences can be selected for editing from any Biologics Annotator Result document - this includes sequences annotated using Antibody Annotator, NGS Antibody Annotator and Single Clone Antibody Analysis.
To export sequences for editing, first select the sequences or cluster rows you would like to edit. If you are unsure what a cluster is, see Understanding "Clusters" for more information.
Tip: our Filtering tool allows you to pull out sequences according to specified criteria, e.g. Gene Family or Score
Once you have selected the sequences you would like to edit, go to the Post-processing > Extract & Edit Sequences dropdown:
This is what the option to extract and edit looks like when selecting sequences from the All Sequences Table:
Note: selecting Translate output will remove the nucleotide sequence - only the amino acid sequence will be editable if this option is chosen.
If you choose to export from a Cluster Table, you will also have the option to extract the top ranked sequence within the cluster by Liability score (Annotate Sequence Liabilities will need to have been selected when running your annotation).
After Running Extract Sequences for Editing, navigate back to the parent folder to locate the sequences ready for editing:
After opening an editable document (see above) there are multiple ways to interact and edit the sequences:
- You can use the buttons along the top to Insert/Replace, Delete, Undo and Redo. This will affect any highlighted sequence, or wherever the cursor is placed:
- Right clicking after highlighting the sequence or placing the cursor allows you to both insert/replace and delete residues or bases:
- You can also interact directly using the keyboard:
- Pressing backspace/delete allows you to delete highlighted residues/bases or delete the sequence before the cursor
- Starting to type allows you to insert residues/bases to replace the highlighted sequence, or insert sequence wherever the cursor is
- Keyboard shortcuts for undo and redo are supported
A dialogue box will prompt you to confirm any changes made, and annotations will be placed on the sequence to indicate the sequence was edited.
Saving and tracking edits
After you have finished editing the sequence(s), click Save Changes in the top left to save a copy of the edited sequence list.
To see the history of edits on a Sequence Document, go the the Info tab. This will display the modification date and time, as well as the user who made the edits:
- Clicking on an annotation will automatically highlight the associated sequence, ready for any editing
- The Sequence Viewer toolbar on the right allows you to hide or display useful information on or next to your sequences, including:
Strategies for editing to improve developability
If when annotating your sequences you chose to turn on finding Sequence Liabilities as well as variants from the reference database, these will be flagged on your sequences as annotations. You can then replace any flagged liabilities with a residue found in the germline gene or template reference sequence.
In the above image, a cleavage motif (DP) liability has been identified. We can see that in the germline sequence, the residues are usually 68A and 69E. We could choose to mutate D68A or P69E to remove this liability.