IMGT/GeneSearch, IMGT/GeneView, IMGT/LocusView and IMGT/CloneSearch Documentation
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• IMGT/GeneSearch allows to search for genes in a locus based on IMGT gene names, functionality or localization on the chromosome.
  
  • IMGT gene names are according the IMGT nomenclature.
  • The definition of functionality is based on the sequence analysis (IMGT Scientific chart).
    
    
• The output of IMGT/GeneSearch comprises for each gene:
  
  • IMGT gene name, functionality, start and end positions of the gene in the locus and clone(s) containing that gene.
    
  • Access to the individual IMGT Repertoire (by clicking on the IMGT gene name only for IG and TR, not for MHC).
    
  • Access to the IMGT flat file (or for MHC to the EMBL flat file) (by clicking on the clone representation).

• The delimitations of each type of gene for the graphical representation in IMGT/GeneSearch (start and end positions) are the following:
  
  
  • V-GENE: from INIT-CODON to the 3' end of the V-NONAMER.
    
  
  
  • D-GENE: from the 5' end of the 5'D-NONAMER to the 3' end of the 3'D-NONAMER.
  
  
  • J-GENE: from the 5' end of the J-NONAMER to the DONOR-SPLICE (splicing occurring before g of "ngt").
  
  
  • C-GENE: from the ACCEPTOR-SPLICE of the exon (splicing occuring after g of "nagnn" ) to the POLYA_SIGNAL inclusive, for a C-GENE with a unique exon,.
    For a C-GENE with several exons, each exon is represented from the ACCEPTOR-SPLICE to the DONOR-SPLICE, except the last exon which is represented from the ACCEPTOR-SPLICE to the POLYA_SIGNAL inclusive.
    
  
  
  • Particularities of the pseudogenes delimitations are indicated in the individual locus documentation.

• IMGT/GeneView allows to view a given gene in a locus.
  
• The output of IMGT/GeneView, for each gene, is similar to that of IMGT/GeneSearch.
  

• IMGT/LocusView allows to view genes in a locus and to zoom on a given area.
  
• The output of IMGT/LocusView for each gene, is similar to that of IMGT/GeneSearch.

• IMGT/CloneSearch provides information on the clones that are used in IMGT/LocusView.
  That information is extracted:
  • from IMGT/LIGM-DB flat files lines:
    - length clone (from the ID line),
    - accession number (from the AC line),
    - overlapping sequences (from of the CC lines)
    - and clone name, cell line, strain, clone library, and IMGT-notes (from the FT lines).
  • from the analyses of overlapping clones in IMGT/GeneSearch, IMGT/GeneView and IMGT/LocusView:
    - position on the locus,
    - clone direction,
    - and overlapping clones. Overlapping clones are only shown if present.

-> IMGT/GeneSearch, IMGT/GeneView, IMGT/LocusView and IMGT/CloneSearch Documentation
-> IMGT/GeneSearch, IMGT/GeneView, IMGT/LocusView and IMGT/CloneSearch Query page

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