VA, VB Format

Although when vaseq and vbseq are provided (for their format requirements, please refer to Amino Acids Sequences Format), these two columns va and vb are not used by our subsequent algorithm, we expect that it would be more convenient for the users to supply the names.

In this section, we provide some general guidelines on the nomenclatures used. Before you get started:

Warning

Make sure that the information provided in the tcr_species column is compatible with the corresponding information in the va and vb columns.

IMGT Nomenclature

During our data curation, we found that there are at least three nomenclatures for TCRs. We choose to use the nomenclature adopted by The International Immunogenetics Information System (IMGT).

Note

Make sure that your nomenclature conforms with the IMGT nomenclature. For correspondence among different nomenclatures, you can refer to this website.

Warning

Information provided in va and vb columns should be

v gene name + allele name

If only gene names are available in your data, we recommend substituting with the corresponding reference alleles.

That being said, we still feel it could be helpful to provide a checklist to overcome some common “issues” we encountered:

va should start with TRAV

vb should start with TRBV

No multiple TCRs in a string

Replace all . with -

Replace all : with *

Strip off all whitespaces:

Change names like TRAV01-01 to TRAV1-1

Make sure both gene names and allele names are provided

If there are only gene names, use their reference alleles e.g. appending *01 to the string

Although we perform basic data curation while reading the user input, it’s nearly impossible for us to cover all corner cases. Therefore, we strongly recommend you to check your input format before preceding to using the main algorithm.

Sample Input

va	vb
TRAV19*01	TRBV9*01
TRAV7-3*04	TRBV1*01

Note

If you are still not sure whether or not the information you supplied conforms with our standard, we also provided some rudimentary functionalities to help you. Please refer to Data Curation where we guide you through the process.