De Novo Sequencing of the CDR3 Region
While the CDR3 of the light chain is mostly encoded by the germline sequences, the CDR3 of the heavy chain is usually not available in databases. It is encoded by the so-called D-segments, but these are modified by nucleases and terminal transferases. Typically, only 1-4 AA of a D-segment remains in the matured antibody. The rest of the D-segment is “artificial” and has to be sequenced de novo. http://www.creative-biolabs.com/next-generation-antibody-sequencing.html