Biologics Tutorial: Add Sequences to the Registry

Documentation: Version 22.3
This tutorial provides step-by-step instructions for adding an antibody, Aducanumab, to the Biologics registry.

Along the way it illustrates:

  • Adding nucleotide sequences to the registry
  • Options for translating protein sequences from the above
  • Entity relationships
  • The protein classification system which detects and annotates protein formats and components
  • Calculated values for new sequences
This topic describes the manual process for adding single entities to the registry in the UI. There are other options for adding entities, including bulk import options, importing GenBank files, and API-based insert methods.

Note that when you create your own entities, the registry names are auto-generated, and therefore may differ from the names shown in these tutorials.

Set Up Trial Server

  • This tutorial assumes that you have registered and created a Biologics Trial instance of the server.
  • If you have already created a biologics trial server, select it, and login: Your Sites

Register a Nucleotide Sequence

We register a sequence composed of a leader sequence + the light chain for Aducanumab.

  • In the header, click the main Menu.
  • Under Registry, click Nucleotide Sequences.
  • On the Nucleotide Sequences page, click Create and select Nucleotide Sequence.
  • On the page Register a New Nucleotide Sequence, fill out the form as follows:
  • Name: Leave this blank for the tutorial.
  • Description: Copy and paste this text:
Signal Peptide 4 + Aducanumab Light Chain. The Light chain sequence of a IgG1 monoclonal antibody, which targets aggregated forms of β-amyloid (Aβ) in the hopes of reducing its buildup. Leader sequence HV103_HUMAN has been added.
  • Alias: Add the two values below. Hit the Tab key to confirm each entry:
Aducanumab Light Chain

HV103_HUMAN
  • Nucleotide Sequence Parents: Leave Blank
  • Sequence: Copy and paste this sequence:
ATGGACTGGACCTGGAGGATCCTCTTCTTGGTGGCAGCAGCAACAGGTGCCCACTCGGATATTCAGATGACCCAGAGCCCGAGCAGCCTGAGCGCGAGCGTGGGCGATCGCGTGACCATTACCTGCCGCGCGAGCCAGAGCATTAGCAGCTATCTGAACTGGTATCAGCAGAAACCGGGCAAAGCGCCGAAACTGCTGATTTATGCGGCGAGCAGCCTGCAGAGCGGCGTGCCGAGCCGCTTTAGCGGCAGCGGCAGCGGCACCGATTTTACCCTGACCATTAGCAGCCTGCAGCCGGAAGATTTTGCGACCTATTATTGCCAGCAGAGCTATAGCACCCCGCTGACCTTTGGCGGCGGCACCAAAGTGGAAATTAAACGCACCGTGGCGGCGCCGAGCGTGTTTATTTTTCCGCCGAGCGATGAACAGCTGAAAAGCGGCACCGCGAGCGTGGTGTGCCTGCTGAACAACTTTTATCCGCGCGAAGCGAAAGTGCAGTGGAAAGTGGATAACGCGCTGCAGAGCGGCAACAGCCAGGAAAGCGTGACCGAACAGGATAGCAAAGATAGCACCTATAGCCTGAGCAGCACCCTGACCCTGAGCAAAGCGGATTATGAAAAACATAAAGTGTATGCGTGCGAAGTGACCCATCAGGGCCTGAGCAGCCCGGTGACCAAAAGCTTTAACCGCGGCGAATGC
  • Annotations: Leave Blank
  • On the bottom right of the page, click Next.
  • On the Confirm tab, review your entries and click Finish.
    • Notice you could also translate a protein sequence immediately but to illustrate the two processes separately, just click Finish for now.
  • The registry nucleotide sequence will be added to the registry. The name of the sequence (in these screenshots "NS-13") may be different in your registry, as we had the name generated automatically. Once a new sequence is added, the registry enforces its uniqueness: if you attempt to register the same sequence twice, you will receive an error message.

Note that you can protect the visibility of both Nucleotide and Protein Sequences in Biologics so that only specific users will ever see the actual sequence itself, while more users have access to the metadata about the sequence. Learn more in this topic:

Translate and Register a Protein Sequence

To translate a protein sequence based on this nucleotide sequence, follow the instructions below.

  • On the Nucleotide Sequences page, click NS-13, or whatever the system has named your new nucleotide sequence.
  • On the nucleotide sequence details page, select Create > Protein Sequences. (Note there are similar workflows available for Constructs and Vectors.)

  • On the page Register a New Protein Sequence, enter the following information in the form:
  • Name: Leave this blank for the tutorial.
  • Description: Leave the automatically entered text unchanged.
  • Alias:
Aducanumab Light Chain
  • Organisms:
Human
  • Protein Sequence Parents: Leave blank. (Use this when parent protein sequences are already in the registry.)
  • Seq Part: Leave blank. (Use this when you know the sequence type, like Leader, Linker, or Tag.)
  • Click Next.
  • On the Sequence tab, click the dropdown Translation Frame and select "1". (Note that selecting "2" or "3" will re-render the sequence preview panes, as will manually refining the Protein Start and End points.)
  • Click Next.
  • The system searches the protein classification library and generates annotations for the sequence parts.
  • Click Next on all remaining screens of the wizard. The wizard shows you calculated information on the following tabs:
  • On the Annotations tab, review the information, and click Next.
  • On the Properties tab, the system calculates a number of physical properties of the protein sequence. Review the information, and click Next.
  • On the Confirm tab, click Finish.
  • The new protein will be added to the registry. The auto-generated name of the new protein (in this case PS-27) may be different in your registry.
  • Click the name of the new protein to see the details page. Under Related Entities, notice the link to the originating nucleotide sequence (NS-13).

Related Topics

Tutorial Curriculum

Biologics Basics: Navigate and Search

Biologics Tutorial: Register Samples

Discussion

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