IMGT: Difference between revisions

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**** on NCBI: http://www.ncbi.nlm.nih.gov/nuccore/4732152?report=graph
**** on NCBI: http://www.ncbi.nlm.nih.gov/nuccore/4732152?report=graph
**** Both look very similar, almost identical information
**** Both look very similar, almost identical information
**** But IMGT has added the numbers of the VDJ fragments
**** Annotations that they add: [http://imgt.org/download/LIGM-DB/ftable_doc.html Ftable]
**** Annotations that they add: [http://imgt.org/download/LIGM-DB/ftable_doc.html Ftable]
** MHC-DB
** MHC-DB

Revision as of 22:19, 15 July 2011

Intro

  • Basic problem: If you have an immune receptor sequence, e.g. antibody or T-Cell receptor, how do you call it?
  • Just like for all other nucleotide sequences: We need
    • submitted sequences (like Genbank)
    • "reference" sequences (like RefSeq)
    • genes (like NCBI Genes), i.e. a collection of reference sequences
    • and people that sort out this whole mess, the IMGT curators
  • IMGT is a 90's generation website, like the genome browser
  • Lots of static webpages, e.g. the new year wishes page

IMGT Structure

  • 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
    • Repertoire: descriptions of loci, genes and 3D-structures
      • Example human IGH [2]
      • Provides nice lists of a loci, with all alleles, types, etc, e.g. human IGV [3]
    • Web Resources: A mixed bag with explanations on how they curate
      • Actually the best starting point