Once a sequence has been imported into Benchling, it is now ready to be visualized and edited. This includes any modified oligos you upload to Benchling.
In the Sequence Map View, individual nucleotides are represented by capital letters that correspond to that nucleotide’s nitrogenous base. Unmodified nucleotides are represented by the light gray circles surrounding the base, while modified nucleotides are represented with symbols:
In the example sequence above, we can see that the Adenine at the 5’ location contains a modified sugar (open purple circle) as well as a modified 3’ phosphate group (black diamond). The specific modifications on this nucleotide can be determined by hovering over an individual nucleotide, which will produce a hover chip containing the specific modifications:
Using the split workspace function, users can view both the Sequence Map of the oligonucleotide sequence and the Nucleotide list simultaneously. Toolbar tabs can be rearranged for either the lefthand or righthand side of the workspace by dragging and dropping the tab on the desired side of the workspace.