Many scientists work with sequences that originate from or are expressed in different host organisms that don’t adhere to the standard codon table. Instead, they translate DNA to amino acid following alternative, or non-standard, genetic codes defined by NCBI.
You can use alternative genetic codes on translations in Benchling to model the relationships between DNA and translated proteins. By default, Benchling uses the standard genetic code unless you set an alternative one or one is defined in an imported GenBank file. You can set genetic codes when creating new translations or editing existing translations..
This article explains how information is converted when importing and exporting Genbank files, how to apply alternative genetic codes to existing translations, and how to create AA sequences from translations that use alternative genetic codes.
How translations and genetic codes are defined when importing and exporting GenBank files
When uploading a GenBank file, Benchling determines what information will be defined as a translation and what will be defined as a genetic code based on the file’s properties and features that define coding sequences (CDS). When exporting, Benchling preserves genetic codes, translations, and annotations.
Importing a GenBank file
When the file is imported, CDS features on the GenBank file create translations on DNA or RNA sequences. Their respective genetic codes are defined by the /transl_table property. If this property isn’t specified on a CDS feature, the translation defaults to the standard genetic code. The example below shows a CDS feature using genetic code 11, taken from thisDNA sequence in GenBank format.
Exporting as a GenBank file
When exporting as a GenBank file:
- Translations export as CDS features
- Annotations export as features with their types as specified in Benchling
- Custom fields export with features
- Genetic codes export as transl_table properties
Apply an alternative genetic code to a translation
To set or change an alternative genetic code on an existing translation:
- Open the sequence and select the translation by clicking its name.
- Click the flag icon in the right-side menu to open the Features panel.
- Alternatively, right-click the translation and select Edit Translation.
- Select the genetic code from the drop-down menu. You can search for genetic codes by name, number, or taxonomy keywords, which are determined by the systematic range for each genetic code as defined by NCBI.
- Click Save. The amino acid residues in the translation update to reflect the selected genetic code.
While a DNA or RNA sequence can have many translations, each translation can have its own genetic code. This means you can model a single DNA or RNA sequence to express many AA sequences using different genetic codes. To create a new translation with an alternative genetic code, visit Creating and analyzing translations.
Apply alternative genetic codes to multiple translations
To apply a genetic code to multiple translations on a sequence:
- Click the flag icon to open the Features panel and click Show expanded view.
- Select the translations, then click the pencil icon in the top-right corner.
- In the pop-up window, select the genetic code from the drop-down menu, then click Save.
Note: A translation from an alternative genetic code will only be linked if there’s already a translation on the sequence with the same genetic code. To learn more about genetic codes and translation links, visit Configure a translation link in your registry.
Create AA sequences from translations with alternative genetic codes
You can create an AA sequence that uses an alternative genetic code directly from the corresponding translation by right-clicking on the translation and selecting Create AA Sequence.
Note: Creating AA sequences from the Create menu creates an AA sequence based on the standard genetic code.
Supported genetic codes
Benchling currently supports all genetic codes defined by NCBI except:
- 27. Karyorelict Nuclear Code
- 28. Condylostoma Nuclear Code
- 31. Blastocrithidia Nuclear Code