IMGT: Difference between revisions

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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?
* 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
* Just like for all other nucleotide sequences: We need  
** submitted sequences (like Genbank)
** "reference" sequences (like RefSeq)
** genes (like NCBI Genes)
** and people that sort this whole mess
* The main reference database for immune loci is IMGT.org
* The main reference database for immune loci is IMGT.org
* It consists of databases, tools and additional files (e.g. ontology, some notes, etc)
* It consists of databases, tools and additional files (e.g. ontology, some notes, etc)
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*** e.g. [http://www.imgt.org/IMGT_GENE-DB/GENElect?query=2+IGHV1-18&species=Homo+sapiens IGHV1-18]
*** e.g. [http://www.imgt.org/IMGT_GENE-DB/GENElect?query=2+IGHV1-18&species=Homo+sapiens IGHV1-18]
*** <positionOnGenome> starts from one and numbers the genes along the chromosome, see [http://genome.ucsc.edu/cgi-bin/hgTracks?insideX=118&revCmplDisp=0&hgsid=202563483&hgt_doJsCommand=&position=chr14%3A106%2C368%2C424-106%2C388%2C490&hgtgroup_map_close=0&hgtgroup_phenDis_close=1&hgtgroup_genes_close=0&hgtgroup_rna_close=0&hgtgroup_expression_close=0&hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_neandertal_close=1&hgtgroup_varRep_close=0 genome browser (switch on encode genes)]
*** <positionOnGenome> starts from one and numbers the genes along the chromosome, see [http://genome.ucsc.edu/cgi-bin/hgTracks?insideX=118&revCmplDisp=0&hgsid=202563483&hgt_doJsCommand=&position=chr14%3A106%2C368%2C424-106%2C388%2C490&hgtgroup_map_close=0&hgtgroup_phenDis_close=1&hgtgroup_genes_close=0&hgtgroup_rna_close=0&hgtgroup_expression_close=0&hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_neandertal_close=1&hgtgroup_varRep_close=0 genome browser (switch on encode genes)]
** Repertoire: all loci with descriptions, e.g. human IGH, human IGK, etc.
** Repertoire: descriptions of loci, genes and 3D-structures
*** Example human IGH [http://www.imgt.org/textes/IMGTrepertoire/LocusGenes/chromosomes/human/IGH/Hu_IGHchrom14.html]
*** Example human IGH [http://www.imgt.org/textes/IMGTrepertoire/LocusGenes/chromosomes/human/IGH/Hu_IGHchrom14.html]
*** Also provides nice lists of a loci, with all alleles, types, etc, e.g. human IGV [http://www.imgt.org/textes/IMGTrepertoire/LocusGenes/index.php?repertoire=genetable&species=human&group=IGHV]
*** Provides nice lists of a loci, with all alleles, types, etc, e.g. human IGV [http://www.imgt.org/textes/IMGTrepertoire/LocusGenes/index.php?repertoire=genetable&species=human&group=IGHV]
** Web Resources: A mixed bag with explanations on how they curate
*** Actually the best starting point

Revision as of 17:11, 12 July 2011

  • 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)
    • and people that sort this whole mess
  • 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
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