This article describes how to use a Name Scheme to enrich your data and simplify analysis. Name schemes can only be created by your organization's administrators, but are available for everyone in the organization to use. For information on what is a Name Scheme see the What Is a Name Scheme and Why Is It Useful? article. For information on how to create a new Name Scheme, see the How to Create a Name Scheme article.
Common uses for Name Schemes include:
- Creating custom columns in analysis results from sequence names, so that those columns can be used for matching when adding Assay Data.
- Defining a unique identifier from sequence names to use for pairing separate Heavy and Light (Lambda or Kappa) chain sequences.
- Defining a unique identifier and optional chain for use when assembling Sanger reads.
Batch Assemble Sanger Sequences
To assemble Sanger sequences using a Name Scheme, first select the Batch by Name Scheme option, then select the name scheme you would like to use from the Name scheme dropdown. Only Name Schemes that contain a field with a Common Identifier type will be available for selection.
The assembly process will apply the Name Scheme to your input sequences by splitting their names by the Name Scheme delimiters, then extracting the Common Identifier and Chain fields (if the latter is present). It will then use the values it encounters for these fields in each sequence as the unique key for assembly. Here is an example with the following sequences:
We have defined a Name Scheme that contains delimiters of _; and two fields for Common Identifier (the second split piece) and Chain (the first split piece). Batch assembly will apply the Name Scheme to our four sequences to create assembly keys of 31023_VH for the first two sequences and 31023_VK for the second two. As these keys will be the same for two sequences each, the Heavy and Kappa sequences will be assembled together as desired.
Output sequences will be named according to the assembly key for readability, but all fields from the Name Scheme will be saved to each sequence for display in downstream results.
Pair Heavy/Light Chains
The Pair/Heavy Light Chains analysis operation allows the selection of a name scheme with a Common Identifier field for pairing sequences using their value for this field. The output of this operation will contain the input sequences that have been paired where they had an identical value for their Common Identifier field.
Let's look at an example to illustrate, suppose we have the following sequences:
and we have defined a Name Scheme with delimiters of _; and a Common Identifier field for the second split piece. When we run the Pair Heavy/Light Chains operation with this Name Scheme, it will split each sequence by the delimiters and determine that both share a common identifier value of 31023. The two sequences will be output paired and shown together as a single row in Antibody Analysis results.
Handy Tip: Antibody Annotator pairs sequences by the Common Identifier field automatically if you have specified a Name Scheme in the Antibody Annotator options (see below). This allows you to skip the Pair Heavy/Light Chains analysis step completely if you wish.
Antibody Annotator can make use of Name Schemes to simplify your workflow. Once you have Batch Assembled your sequences using a Name Scheme (if this is required), you can proceed directly to Antibody Annotator which will recognise that you have already associated your sequences with a Name Scheme and make use of the name scheme fields automatically. It will pair Heavy and Light chains using the Common Identifier field in your Name Scheme. It will also save all Name Scheme display fields so they are visible as columns in the results.
If your data does not require assembly, you can proceed straight to Antibody Annotator using your raw sequences and specify a Name Scheme with a Common Identifier field. This will be used to pair the sequences by chain if you select the Both chains in associated sequences option for Selected sequences are:. All fields from the selected Name Scheme will be visible as columns in the results.