View a translation
To create a translation for a selected DNA sequence, highlight a section of the plasmid on the left side sequence map, and right-click. Click Create Translation and then Forward to view the forward translation for that selection. The translate will show up in line with your DNA sequence.
Create a translation
Open a DNA sequence. Hover over the an annotation that you wish to translate, and select it. Alternatively, manually select a region of your bases.
Click Create at the top of your sequence map, then click Translation. Select the reverse strand as the coding strand.
You can also right-click on the selection, and click Create Translation.
Your translation will automatically be indexed. If your translation isn't indexed or you want to remove the indexing, click on the gear icon in the top right and toggle "Amino Acid indices".
Keep indices continuous between two translations by linking translations. Click on the annotations icon and open Expanded Translations. Press the checkboxes and click Link Translations to link two translations.
Alternately, right-click on any translation to Link Previous Translation and create or add it to the translation group.
Analyze a translation
Right-click directly on your translation and click Analyze as Translation.
Benchling will display any biochemical properties for that translation. Specifically, you'll see the following properties:
Translation position relative to the DNA sequence
Molecular weight of the resulting protein
The protein's isoelectric point (pI)
Amino acid frequencies in the translation
Create an Amino Acid Sequence
To create a separate amino acid sequence map from a translation overlaid on a DNA sequence, right-click the translation and select "Create AA Sequence". Choose a folder and name for your new amino acid and then click "Create". Creating a separate amino acid file in Benchling will allow you to update protein-specific viewing options such as coloring scheme, CDR annotations and liability sites.
What do the colors of amino acids mean?
We support three coloring schemes. The default is RasMol. Details of the coloring schemes are described below:
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.
Polarity: Yellow means non-polar, green means polar uncharged, red means polar acidic, and blue means polar basic.
Hydrophobicity: The residues are colored on a spectrum from red to blue, where red means the most hydrophobic and blue means the most hydrophilic.
Once you've completed this tutorial you may want to learn about creating and linking a protein translation next.