Vdjdb-splash.png

Software Formats
1

Saw this figure from vdjdb-db github. GitHub - antigenomics/vdjdb-db at 2017-03-18
It’s useful to show the connections among CDR3s and antigen epitopes but how to make this plot?

2

Firstly I’d like not note that this graph was made mainly for aesthetic purposes. The graph was visualized in Cytoscape, the edges and nodes were assigned as follows:

  • All epitopes like CMV-NLV were added as nodes
  • All CDR3 amino acid sequences were also added to the plot together with edges connecting them to the epitopes they recognize
  • CDR3 sequences that differ by no more than 3 (as far as I remember) substitutions were connected with edges
3

Thanks for sharing! I would love to have a try!