Available in:
Biologics LIMS
This topic covers how to register a new nucleotide sequence using the graphical user interface. To register using the API, or to bulk import sequences from an Excel spreadsheet, see
Use the Registry API.
Nucleotide Sequence Validation
For nucleotide sequences, we allow DNA and RNA bases (ACTGU) as well as the
IUPAC notation degenerate bases (WSMKRYBDHVNZ). On import, whitespace will be removed from a nucleotide sequence. If the sequence contains other letters or symbols, an error will be raised.
For protein sequences, we only allow standard amino acids letters and zero or more trailing stop codon '*'. On import, whitespace will be removed from a protein sequence. If the sequence contains stop codons in the middle of the sequence or a other letters or symbols, an error will be raised.
When translating a nucleotide codon triple to a protein sequence, where the codon contains one or more of the degenerate bases, the system attempts to find a single amino acid that could be mapped to by all of the possible nucleotide combinations for that codon. If a single amino acid is found, it will be used in the translated protein. If not, the codon will be translated as an 'X'.
For example, the nucleotide sequence 'AAW' is ambiguous since it could map to either 'AAA' or 'AAT' (representing Lysine and Asparagine respectively), so 'AAW' will be translated as an 'X' However, 'AAR' maps to either 'AAA" or 'AAG' which are both are translated to Lysine, so it will be translated as a 'K'.
Create a Nucleotide Sequence
To add a new nucleotide sequence to the registry:
- Open the Nucleotide Sequence page, then select Add > Add manually.
- From an existing protein sequence's details page, select Manage > Register Nucleotide Sequences to register a new nucleotide sequence and connect it as that protein's source.
The creation wizard has two tabs:
Details
On the
Register a new Nucleotide Sequence page, in the
Details panel, populate the fields:
- Name: Provide a name, or one will be generated for you. Hover to see the naming pattern
- Description: (Optional) A text description of the sequence.
- Alias: (Optional) Alternative names for the sequence. Type a name, click enter when complete. Continue to add more as needed.
- Common Name: (Optional) The common name for this sequence, if any.
- Nucleotide Sequence Parents: (Optional) Parent components. A related sequence the new sequence is derived from, for example, related as a mutation. You can select more than one parent. Start typing to narrow the pulldown menu of options. If the parent you want isn't registered yet, select Add new; see Register Molecules for details on how this works.
- Sequence: The nucleotide sequence
- Check Sequence is known, if you can enter the sequence now.
- Check Sequence is unknown, if you want to enter the sequence later. See Unidentified Sequences for details on working with unknown sequences.
- If the sequence you enter matches one already registered, a message identifies the existing nucleotide sequence. If you reached this wizard from a protein sequence's Manage > Register Nucleotide Sequences action, click Associate to connect the existing nucleotide sequence to that protein instead of creating a duplicate.
- Annotations: (Optional) A comma separated list of annotation information:
- Name - a freeform name
- Category - region or feature
- Type - for example, Leader, Variable, Tag, etc.
- Start and End Positions are 1-based offsets within the sequence.
- Description
- Complement
Click
Next to continue.
Confirm
Review the details on the
Confirm tab.
Options to complete registration:
- Finish: Register this nucleotide sequence and exit.
- Finish and translate protein: Both register this nucleotide sequence and register the corresponding protein. This option will take you to the registry wizard for a new protein, prepopulating it with the protein sequence based on the nucleotide sequence you just defined.
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