Information Technology Reference
In-Depth Information
users to view genes at their loci and then zoom in on a selected area. IMGT/GeneView
allows users to directly view a given gene at a locus. IMGT/GeneSearch and
IMGT/CloneSearch allow retrieval of information concerning genes and clones, re-
spectively, analysed in IMGT/LocusView. IMGT/GeneSearch allows searching for
genes at a locus, based on IMGT gene names, functionality, or chromosomal localiza-
tion. IMGT/CloneSearch provides information on the clones that were used to build the
locus contigs displayed in IMGT/LocusView (accession numbers are from IMGT/
LIGM-DB, gene names from IMGT/GENE-DB, and clone position and orientation,
and overlapping clones from IMGT/LocusView). IMGT/GeneInfo provides informa-
tion on potential human and mouse TR rearrangements (Baum, Hierle, Pascal, Bel-
lahcene, Chaume, Lefranc, Jouvin-Marche, Marche, and Demongeot 2006).
IMGT/GeneFrequency is an IMGT interactive tool that dynamically computes histo-
grams which represent the contribution of individual V, D, and J genes in sets of ex-
pressed IG and TR rearranged V-(D)-J sequences in IMGT/LIGM-DB.
IMGT/GeneFrequency results are obtained by querying IMGT/LIGM-DB for se-
quences which are selected, for example, on the specificity criteria.
1.3.3 IMGT
®
Genome Web Resources
The IMGT
®
genomic Web resources are compiled in the IMGT Repertoire “Locus
and genes” section that includes Chromosomal localizations, Locus representations,
Locus description, Gene exon/intron organization, Gene exon/intron splicing sites,
Gene tables, Potential germline repertoires, the complete lists of human and mouse
IG and TR genes, and the correspondences between nomenclatures (Lefranc and
Lefranc 2001a; Lefranc and Lefranc 2001b). The IMGT Repertoire “Probes and
RFLP” section provides data on probes used in Southern analysis and on gene inser-
tion/deletion polymorphisms (Osipova, Posukh, Wiebe, Miyazaki, Matsumoto,
Lefranc, and Lefranc 1999; Dard, Lefranc, Osipova, and Sanchez-Mazas 2001;
Elemento, Gascuel, and Lefranc 2002; Lefranc and Lefranc 2004).
1.4 IMGT-ONTOLOGY Concepts and IMGT
®
Components
for Genetics
1.4.1 IMGT
®
Sequence Databases
The IMGT
®
genetic approach refers to the study of genes in relation to their polymor-
phisms, mutations, expression, specificity, and evolution. The IMGT
®
genetics
approach heavily relies on the DESCRIPTION concept (and particularly on the
V-REGION, D-REGION, J-REGION, and C-REGION core concepts for the IG and
TR), on the CLASSIFICATION concept (gene and allele concepts), and on the
NUMEROTATION concept (IMGT unique numbering) (Lefranc 1997; Lefranc 1999;
Ruiz and Lefranc 2002; Duprat and Lefranc 2003; Lefranc, Pommié, Ruiz, Giudicelli,
Foulquier, Truong, Thouvenin-Contet, and Lefranc 2003; Lefranc, Pommié, Kaas,
