IMGT Bloc-notes

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The IMGT Genome page

The IMGT Genome page provides links to databases and resources, and nomenclatures on the genome from human, model animal species and domestic species.

Editors: Marie-Paule Lefranc and Gérard Lefranc (LIGM, Université Montpellier 2, CNRS, Montpellier, France)

Human

• Databases
  • IMGT/3Dstructure-DB, gene and allele identification of immunoglobulins (IG), T cell receptor (TR) and MH with known 3D structure, Montpellier, France.
  • IMGT/GENE-DB, database of human immunoglobulin (IG) and T cell receptor (TR) genes, Montpellier, France.
  • IMGT/LIGM-DB, nucleotide sequence database of immunoglobulin (IG) and T cell receptor (TR), Montpellier, France.
  • IMGT/MHC-DB, sequence database, EBI, UK.
  • IMGT/PRIMER-DB, database of oligonucleotides for immunoglobulins (IG) and T cell receptors (TR), Montpellier, France.
• Resources
  • Atlas of Genetics and Cytogenetics in Oncology and Haematology
  • Ensembl Genome Browser, The Sanger Institute and EBI
  • GeneMap'99
  • GeneSeeker
  • Genew
  • Human Genome Browser Gateway, UCSC Genome Browser
  • Human Genome Resources, NCBI
  • IG and TR loci: Positions on chromosomes (IMGT Repertoire)
  • IMGT Genes on the Ensembl Genome Browser
  • Other links in IMGT Bloc-notes Resources for the human genome
• Nomenclature
  • HGNC, HUGO Gene Nomenclature Committee
  • IMGT-NC, IMGT Nomenclature Committee, part of IMGT®, the international ImMunoGeneTics information system®, Montpellier, France.
• References
  • Chromosome 22
    • Ensembl Project - Human integrated resource, EBI/SANGER
    • Genome Catalog, ORNL
    • HUGO Chromosomes, HUGO, Resources : DNA, chromosome, diseases...
    • Human Chromosome 22 and Syntenic Mouse Genomic Sequencing
    • IMGT®, the international ImMunoGeneTics information system®, Human IGL locus, Montpellier, France.
    • LaunchPad, HGMIS
    • Map View, NCBI
    • SpliceNest
    • Dunham, I. et al., The DNA sequence of human chromosome 22, Nature, 489-495 (1999)
• FAQ
  • How is the human genome assembly at NCBI or Ensembl representative of a 'human genome'?
    • The human genome assembly at NCBI or Ensembl has to be considered as a 'virtual frame'. No single individual would never have that genome. Combination of SNPs (for any locus) can only be considered as 'true' if they were confirmed on a single chromosome (or haplotype) of an individual. Even if genome assembly is done from DNA of a single individual it remains that the assignment to one or the other chromosome is still an issue that may result in 'mixed' haplotype. The only definitive answer for haplotypes at the chromosome level is the sequencing of spermatozoon DNA.

Model animal species

• Mouse
  • Resources
    • MGI, Mouse Genome Informatics, The Jackson Laboratory, USA
    • The IMGT Veterinary page: Mouse (Mus musculus)
  • Nomenclature
    • HGNC, HUGO Gene Nomenclature Committee
    • IMGT-NC, IMGT Nomenclature Committee, part of IMGT®, the international ImMunoGeneTics information system®, Montpellier, France.
• Rat
  • Resources
    • The IMGT Veterinary page: Rat
  • Databases
    • RatMap, The Rat Genome Database, rat genes, DNA markers, QTLs, etc. that is localized to chromosome.
    • RGD, Rat Genome Database
  • Nomenclature
    • HGNC, HUGO Gene Nomenclature Committee
    • IMGT-NC, IMGT Nomenclature Committee, part of IMGT®, the international ImMunoGeneTics information system® Montpellier, France.
    • RGNC, Rat Genome and Nomenclature Committee, responsible for the 23 Single Rat Chromosome Committee (SRCC).

Data integration

• myScience research environment, Applied Biosystems, Gene expression: TaqMan® Gene Expression Assays, SNP Genotyping: TaqMan® SNP Genotyping Assays, Gene search: search genes and view genomic products.
• Cytoscape,an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
• BioMOBY, an international research project involving biological data hosts, biological data service providers, and coders whose aim is to explore various methodologies for biological data representation, distribution, and discovery.

Other links

• GNF SymAtlas, Genomics Institute of the Novartis Research Foundation
• The IMGT Veterinary page for the genomes of domestic, model and wild life species

Created: 20/02/2003
Last updated: Wednesday, 04-Jan-2012 22:01:33 CET
Author: Marie-Paule Lefranc
Editors: Valérie Thouvenin-Contet, Chantal Ginestoux
Contact: Marie-Paule Lefranc

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Software material and data coming from IMGT server may be used for academic research only, provided that it is referred to IMGT®, and cited as "IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)." References to cite: Lefranc, M.-P. et al., Nucleic Acids Research, 27, 209-212 (1999) Cover of NAR; Ruiz, M. et al., Nucleic Acids Research, 28, 219-221 (2000); Lefranc, M.-P., Nucleic Acids Research, 29, 207-209 (2001); Lefranc, M.-P., Nucleic Acids Res., 31, 307-310 (2003); Lefranc, M.-P. et al., In Silico Biol., 5, 0006 (2004) [Epub], 5, 45-60 (2005); Lefranc, M.-P. et al., Nucleic Acids Res., 33, D593-D597 (2005) Full text; Lefranc, M.-P. et al., Nucleic Acids Research 2009 37: D1006-D1012; doi:10.1093/nar/gkn838 Full text.
For any other use please contact Marie-Paule Lefranc Marie-Paule.Lefranc@igh.cnrs.fr.

     

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