Creating and analyzing translations

You can translate DNA and RNA sequences, create amino acid (AA) sequences, and generate biochemical properties for translations.

This article goes over how to access the translations list, and from there, create, analyze, and add to translations. 

Access the translations list

Create, view, and delete annotations in the Features panel and its expanded view. To access the Features panel, click the flag icon in the right-side menu.

You can view all the translations on a sequence in a larger window by clicking Show Expanded View in the Features panel. This opens a full list of translations in a Translations tab where you can more easily view and manage them.

Create a translation

To create a translation for a DNA or RNA sequence:

1. Highlight your region of interest or annotation on the DNA.

2. On the Features panel click the Create New at the top of the panel.

   • Alternatively, you can select a region or an annotation on the sequence, right-click, and select Create Translation

3. Enter the translation name, genetic code, strand direction, notes, and custom fields.

4. Click Save.

The translation is automatically indexed. If the translation isn't indexed or to remove the indexing, click the gear icon in the top-right corner and toggle Amino Acid indices.

Add to an existing translation

1. Highlight your region of interest or annotation on the DNA.

2. On the Features panel click Create New at the top of the panel.

   • Alternatively, you can select a region or an annotation on the sequence, right-click, and select Create Translation

3. Click the Add to existing button in the middle of the panel.

4. Select the Forward or Reverse strand.

5. Select the existing translation using the Add as region to dropdown.

6. Click Save.

Regions of a translation cannot be edited once saved. Regions of a translation can be deleted from the Features panel or from the expanded view Translations tab.

When adding a translation that uses a non-standard genetic code on a DNA sequence map, an existing translation with a non-standard genetic code has to be present.

Analyze a translation

To view a translation’s biochemical properties, right-click a translation and select Analyze Translation. If a translation has a non-standard genetic code, the biochemical properties will reflect the translation using non-standard genetic code. These biochemical properties will be analyzed:

• Amino acid frequencies

• Net Charge

• Extinction coefficients

• Instability index

• Molecular weight of the resulting protein

• The protein's isoelectric point (pI)

• Translation position relative to the sequence

Create an amino acid sequence from a translation

Creating separate amino acid entities enables customized protein-specific viewing options such as color scheme, CDR annotations, and liability sites.

To create an amino acid sequence map from a translation on a DNA or RNA sequence:

1. Right-click the translation and select Create AA Sequence.

2. Select a folder, a new name, and a schema for the AA sequence.

3. Click Create.

If the translation corresponds to a non-standard genetic code, an AA sequence identical to the translation and its non-standard genetic code will be created.

Amino acid colors

The default color scheme in Benchling is RasMol, however, Benchling supports three color schemes:

• RasMol: This coloring scheme is traditional, and groups amino acids by property. In general, polar residues are brighter colors, while non-polar residues appear more subdued.

• Hydrophobicity: The residues are colored on a spectrum from red to blue, where red means hydrophobic and blue means hydrophilic.

• Polarity: Colors indicate specific polarities:

  • Red: polar acidic

  • Yellow: non-polar

  • Green: polar uncharged

  • Blue: polar basic

You can change the color scheme by clicking on the gear icon and selecting the wrench icon next to Coloring Scheme.