Antibodies from GenBank®

  • Individual antibody sequences accompanying publications are oftentimes deposited in public sequence repositories such as GenBank®.

  • Extracting antibody sequences either by sequence matches or by text search can be cumbersome as GenBank® is all-encompassing* and therefore not customized for antibody sequences specifically.

  • We extracted the antibody sequences from GenBank and connected these to the documents they were associated with (e.g. publications via PMID) in a service called

  • AbGenBank www.naturalantibody.com/abgenbank

  • We only keep the antibody sequences where we identified all three CDRs and all four framework regions containing only the 20 canonical amino acids.

  • Antibody sequences in AbGenBank can be identified by either searches of full variable region sequences or individual IMGT-defined** CDRs.

  • Antibodies associated with specific targets can be identified via text-search (Figure 1).

References

1 Eric W Sayers, Mark Cavanaugh, Karen Clark, James Ostell, Kim D Pruitt, Ilene Karsch-Mizrachi, GenBank, Nucleic Acids Res. 2019 Jan 8;47(D1):D94-D99. doi: 10.1093/nar/gky9892. Marie-Paule Lefranc. Unique database numbering system for immunogenetic analysis. Immunol Today. 1997 Nov;18(11):509. doi: 10.1016/s0167-5699(97)01163-8.

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