The Scaffold annotator may be used to analyse a small number of sequences (produced by low throughput sequencing) based on predefined scaffolds.
To set up your Scaffold annotator analysis, select your sequences or sequence list in your folder, click Annotation and select Scaffold annotator in the dropdown.
To run a scaffold analysis, several options need to be configured in the Scaffold annotator popup, including:
- Scaffold* - Scaffolds are utilized by the pipeline for sequence regions, annotations, and validations specifications. Therefore, a scaffold is required to run an analysis.
- Name scheme - This can be set to Ignore filename if not of interest and this will not affect the output results.
- Reference Database* - Reference sequence is utilized by the pipeline to annotate your input sequences. Therefore, a reference sequence is required to run an analysis.
- Numbering Scheme - This is used to number antibody amino acid sequences. We currently support Standard, Kabat and IMGT numbering schemes.
- Genetic Code - Geneious Biologics supports a range of genetic codes which can be chosen from the drop-down menu.
Required options to run an analysis are marked with an asterisk (*). Only Admin users can add Scaffolds, Reference sequence, Primer sets, and Naming schemes. This means that before running any analysis with the Scaffold annotator analysis, an administrator will need to set these up so that all members can access the required information.
Once the Scaffold annotator has been set up, you can run the analysis by clicking Run. Once the analysis starts, a spinner indicating progress will be observable in the Jobs tab and the result will appear in the same folder where the files were selected.
Note that you can select more than one reference sequences by holding down the Ctrl button while selecting the reference sequences.