IMGT/GeneFrequency Documentation LOGO IMGT

http://www.imgt.org



Citing IMGT/GeneFrequency : Lefranc, M.-P. et al., In Silico Biol., 5, 0006 (2004) [Epub], 5, 45-60 (2005). In Silico Biol., 5, 0006 (2004) Abstract
LOGO GeneFrequency
Program version: 1.1.0 (10/01/2011)




Introduction


IMGT/GeneFrequency Search page

BALL In the IMGT/GeneFrequency Search page, the selection takes place in three stages:
  1. Select a Species:

    At present only Homo sapiens and Mus musculus sequences are available.

    SearchPageSpecies

  2. Histogram for:

    • All IMGT/LIGM-DB rearranged sequences
    • or Specificity (choice in a multiple list, for example "anti-thyroid peroxidase (TPO)")

    HAND Following the specificity choice, only the loci that contain genes which answer the selected specificity will be offered for selection in the "Individual locus" box.

    SearchPageHisto

  3. Select Loci:

    1. IG or TR loci:

      • IGH, IGK, IGL, for immunoglobulin
      • TRA/TRD, TRB, TRG, for T cell receptor

      The scale depends on the locus length.

    2. Individual locus:

      • IGH
      • IGK
      • IGL
      • TRA/TRD
      • TRB
      • TRG

    Two different scales (200 kb per line or 400 kb per line) are available, select a scale to visualize the locus.

    SearchPageLoci

  4. Click on the "Search" button to valid your search.

IMGT/GeneFrequency results

BALL Results for All IMGT/LIGM-DB rearranged sequences (IG or TR loci)

The IMGT/GeneFrequency results for all IMGT/LIGM-DB rearranged sequences (IG or TR loci) query comprise:

SummaryIGorTR

BALL Results for All IMGT/LIGM-DB rearranged sequences (Individual locus)

The selected locus (IGH, IGK, IGL, TRA/TRD, TRB or TRG ) is displayed depending on the selection, and in the chosen scale (200 kb or 400 kb).
The IMGT/GeneFrequency results for "Individual locus" query comprise:

IndividualLocus
IndividualLocusZoom



BALL Results for Specificity (IG or TR loci)

The IMGT/GeneFrequency results for selected specificity (IG or TR loci) query comprise:


anti-DNA-IGorTR_Info


BALL Results for specificity (Individual locus)

The selected locus (IGH, IGK, IGL, TRA/TRD, TRB or TRG ) is displayed depending on the selection, the chosen specificity and in the chosen scale (200 kb or 400 kb).
The IMGT/GeneFrequency results for "Individual locus" query comprise:


anti-DNA-IGH_Info

BALL Access to IMGT/LIGM-DB and IMGT/GENE-DB:

Clicking on the vertical bar of a gene gives access to a link to IMGT/GENE-DB entry for that gene an to a list of IMGT/LIGM-DB accession numbers answering to the user selection.
Each IMGT/LIGM-DB accession number has a link to the resulting page in IMGT/LIGM-DB and the IMGT/GENE-DB entry for the gene has a link to the resulting page in IMGT/GENE-DB.

BALL Particularities of the IGK locus:


See also:
References:

[1] Lefranc, M.-P., Nucleic Acids Res., 33, D593-D597 (2005), PMID:15608269, LIGM:291.
[2] Giudicelli V., Protat C., and Lefranc M.-P., The IMGT strategy for the automatic annotation of IG and TR cDNA sequences: IMGT/Automat, European Conference on Computational Biology ECCB 2003
[3] Lefranc, M.-P. and Lefranc, G., The Immunoglobulin FactsBook, Academic Press, 458 pages (2001) ISBN:012441351X
[4] Lefranc, M.-P. and Lefranc, G., The T cell receptor FactsBook, Academic Press, 398 pages (2001) ISBN:0124413528


IMGT/GeneFrequency implementation and developments

The IMGT/GeneFrequency tool was implemented using Perl (CGI, GD, SOAP, DBI, DBD) (DESS Bioinformatique, Université Montpellier II, France, stage at LIGM, Montpellier 14/04/03-31/08/03).

IMGT/GeneFrequency Documentation was written by Stéphanie Jeanjean, Elodie Boucomont (1ère année DUT Génie Biologique option Bioinformatique, IUT Clermont-Ferrand, antenne Aurillac, stage at LIGM, Montpellier 01/07/03-15/08/03) and François Ehrenmann Francois.Ehrenmann@igh.cnrs.fr.

The IMGT/GeneFrequency tool has been improved by François Ehrenmann and Marie-Paule Lefranc for an easier access on the web in July 2006.