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/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 and IMGT/LocusView first version has been developed on the human IGL locus, by Richard D'Agata, Isabelle Gourdon, Nicolas Moyroud, Christine Tranchant (DESS IAO, Université Montpellier II, Montpellier, France, march 2001).
IMGT/GeneSearch, IMGT/GeneView and IMGT/LocusView was developed by Joumana Jabado Michaloud (DESS IAO, Université Montpellier II, Montpellier France).
The IMGT/CloneSearch tool was implemented using Perl (CGI, LWP) programs by Stéphanie Jeanjean (DESS Bioinformatique, Univeristé Montpellier II, France).
Elodie Boucomont (1ère année DUT Génie Biologique option Bioinformatique, IUT Clermont-Ferrand,
antenne Aurillac, stage at LIGM, Montpellier 01/07/03-15/08/03)
contributed to the IMGT/CloneSearch first developments.
