Using Bioinformatics Tools for the Sequence Analysis of Immunoglobulins and T Cell Receptors

Marie‐Paule Lefranc1

1 IMGT, Université Montpellier II, CNRS, Montpellier
Publication Name:  Current Protocols in Immunology
Unit Number:  Appendix 1W
DOI:  10.1002/0471142735.ima01ws71
Online Posting Date:  March, 2006
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Abstract

The huge potential repertoire of 1012 immunoglobulins and 1012 T cell receptors per individual results from complex mechanisms of combinatorial diversity between the variable (V), diversity (D), and junction (J) genes, nucleotide deletions and insertions (N‐diversity) at the junctions and, for the immunoglobulins, somatic hypermutations. The accurate analysis of rearranged immunoglobulin and T cell receptor sequences, and the annotation of the junctions, therefore represent a huge challenge. The IMGT Scientific chart rules, based on the IMGT‐ONTOLOGY concepts, were the prerequisites for the implementation of the IMGT/V‐QUEST and IMGT/JunctionAnalysis tools. IMGT/V‐QUEST analyzes germline V and rearranged V‐J or V‐D‐J nucleotide sequences. IMGT/JunctionAnalysis is the first tool that automatically analyzes the complex junctions in detail. These interactive tools are easy to use and freely available on the Web (http://imgt.cines.fr), either separately or integrated.

Keywords: IMGT; immunoglobulin; T cell receptor; rearrangement; immunogenetics; immunoinformatics; junction analysis; sequence diversity; Collier de Perles; variable gene; variable domain; IMGT/V‐QUEST; IMGT/JunctionAnalysis

     
 
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Table of Contents

  • IMGT Standardized Rules
  • JUNCTION
  • IMGT/V‐QUEST
  • Conclusion
  • Abbreviations Used in this Appendix
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

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Literature Cited

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   Lefranc, M.‐P., Giudicelli, V., Kaas, Q., Duprat, E., Jabado‐Michaloud, J., Scaviner, D., Ginestoux, C., Clément, O., Chaume, D., and Lefranc, G. 2005a. IMGT, the international ImMunoGeneTics information system. Nucl. Acids Res. 33:D593‐D597.
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   Ruiz, M. and Lefranc, M.‐P. 2002. IMGT gene identification and Colliers de Perles of human immunoglobulins with known 3D structures. Immunogenetics 53:857‐883.
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Key References
   Lefranc and Lefranc, 2001a. See above.
  These two books are the prime references for all functional and ORF immunoglobulin and T cell receptor genes and alleles in humans. Genes and alleles are classified and described according to the IMGT Scientific chart rules, based on the IMGT‐ONTOLOGY concepts. Corresponding sequences have been used for the setting up of the IMGT reference directory sets used by IMGT/V‐QUEST and IMGT/JunctionAnalysis.
   Lefranc and Lefranc, 2001b. See above.
Internet Resources
   http://imgt.cines.fr
  Web site of IMGT
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