IMGT

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  • Basic problem: If you have an immune receptor sequence, e.g. antibody or T-Cell receptor, how do you call it?
  • Just like genomes: We need "reference" sequences and people that choose them
  • The main reference database for immune loci is IMGT.org
  • It consists of databases, tools and additional files (e.g. ontology, some notes, etc)
    • LIGM-DB: Nucleotide sequences of all kinds. Can be C, V, J, D, or combinations thereof.
    • MHC-DB
      • Also pulls in from Genbank, changes their identifiers
      • Maps Genbank sequences to MHC-"clusters" of sequences
      • E.g. GQ240381 is annotated as a sequence of HLA06329 [1]
    • GENE-DB: A list of categorized VDJC sequences and all their alleles
      • Naming is <locus><type><number>-<number>*allel
      • e.g. IGHV1-18
    • Repertoire: all loci with descriptions, e.g. human IGH, human IGK, etc.
      • Example human IGH [2]