Note: Translation link type fields require exact DNA → AA translation matches. These link type fields are useful for the validation of DNA-AA paired entities (i.e. if the two do not match, the entity cannot be registered)
Translation links are specialized metadata fields which create DNA → AA linkages in the Registry. They are available exclusively for DNA-based entity schemas, and can be used to track linkages to registered amino acid sequences that are encoded for by stretches of that DNA sequence.
A translation link behaves similarly to an entity link, but includes some additional validation that must pass before the sequence entity can be registered. Translation link fields require that the linked AA entity can be validly translated on any of the 6 reading frames of the DNA sequence entity, or else the sequence will fail validation - and thereby be unable to be registered.
To create a translation link in a schema, first create a field. In this example, we are creating a "Translation Link" field on a "Plasmid" entity.
For the field type, select "Translation." You will see that eligible schemas (i.e. AA schemas) are listed. In this case, we will be creating a translation link to the "Chain" schema.
When registering an entity with a schema that includes a translation link, you must first fill in a valid registered AA sequence into that translation link field. You can either choose to manually fill in the translation link field, or use the Auto-Fill Translation option to have Benchling automatically detect registered AA entities of your desired schema that can be translated from the DNA sequence you are Auto-Filling.
To manually fill in a translation link for your soon-to-be registered plasmid, click in the translation link field and search for the AA sequence you would like to link by name. When you have selected it, the entity will show up as a blue chip in the field.
To use Auto-Fill Translations, click the blue “Auto-Fill Translations” button. Benchling will look across all 6 reading frames of the DNA sequence for any subregion that can be translated to match a registered AA of the schema type specified in the Translation Link field(s).
After filling your translation link field, you can now press “Register” to create your new entity and have Benchling validate that a translated portion of your plasmid sequence does indeed match the AA residues of the linked protein sequence.
If the sequences do not match, an "Invalid link" message will appear in the schema field. You will also notice a message informing you that you are unable to register the entity unless all validation errors are fixed.
We always use the standard genetic code for creating translation links unless a translation with an alternative genetic code already exists on the sequence.