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IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs

M. Y. Monod, V. Giudicelli, D. Chaume, M.-P. Lefranc
2004 Bioinformatics  
Results: IMGT/JunctionAnalysis is the first tool for the detailed analysis of the IG and TR complex V-J and V-D-J JUNC-TION(s).  ...  Motivation: To create the enormous diversity of 10 12 immunoglobulins (IG) and T cell receptors (TR) per individual, very complex mechanisms occur at the DNA level: the combinatorial diversity results  ...  ACKNOWLEDGEMENTS We thank Gérard Lefranc for helpful discussion. We are deeply grateful to the IMGT team for its expertise and constant motivation.  ... 
doi:10.1093/bioinformatics/bth945 pmid:15262823 fatcat:rxsrszb4cncepdc2mvk5blr44a

IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis

V. Giudicelli, D. Chaume, M.-P. Lefranc
2004 Nucleic Acids Research  
Moreover, IMGT/V-QUEST can interact with IMGT/JunctionAnalysis for the detailed description of the V-J and V-D-J junctions, and with IMGT/PhyloGene for the construction of phylogenetic trees.  ...  IMGT/V-QUEST, for 'V-QUEry and STandardization', is an integrated software program which analyses the immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide sequences.  ...  We are deeply grateful to the IMGT team for its expertise and constant motivation and specially to our curators for their hard work and enthusiasm.  ... 
doi:10.1093/nar/gkh412 pmid:15215425 pmcid:PMC441550 fatcat:ir5dt7atazdzlfhbn3iqdmmgqa

IMGT® databases, web resources and tools for immunoglobulin and T cell receptor sequence analysis, http://imgt.cines.fr

M-P Lefranc
2003 Leukemia  
IMGT expertly annotated data and tools described in this paper are particularly useful for the analysis of the IG and TR rearrangements in leukemia, lymphoma and myeloma, and in translocations involving  ...  IMGT, the international ImMunoGeneTics database  (http://imgt.cines.fr), is a high-quality integrated information system specializing in immunoglobulins (IG), T cell receptors (TR) and major histocompatibility  ...  I am deeply grateful to the IMGT team for its expertise and constant motivation.  ... 
doi:10.1038/sj.leu.2402637 pmid:12529691 fatcat:5ox3ssah5vgofeoimrjedjqgeu

IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis

X. Brochet, M.-P. Lefranc, V. Giudicelli
2008 Nucleic Acids Research  
IMGT/ V-QUEST integrates IMGT/JunctionAnalysis for a detailed analysis of the V-J and V-D-J junctions, and IMGT/Automat for a full V-J-and V-D-J-REGION annotation.  ...  IMGT/V-QUEST is the highly customized and integrated system for the standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide sequences.  ...  ACKNOWLEDGEMENTS We are grateful to Vincent Ne`gre and to the IMGT team for its expertise and constant motivation.  ... 
doi:10.1093/nar/gkn316 pmid:18503082 pmcid:PMC2447746 fatcat:djdtm3sveret7coyse2mfmrfli

From IMGT-ONTOLOGY to IMGT/HighVQUEST for NGS Immunoglobulin (IG) and T cell Receptor (TR) Repertoires in Autoimmune and Infectious Diseases

Giudicelli V
2015 Autoimmune and Infectious Diseases Open Access  
IMGT/HighV-QUEST, the high throughput version of IMGT/V-QUEST and IMGT/Junction Analysis, created in 2010, is the first and, so far, the only online portal for analysis of the immunoglobulin and T cell  ...  or antibodies and T cell receptors, expressed by B cells and T cells, respectively.  ...  IMGT® is member of the International Medical Informatics Association (IMIA) and of the Global Alliance for Genomics and Health (GA4GH).  ... 
doi:10.16966/2470-1025.103 fatcat:fvfpxkbe2jbyvg5w6thbw2n5xm

IMGT-Choreography for immunogenetics and immunoinformatics

Marie-Paule Lefranc, Oliver Clement, Quentin Kaas, Elodie Duprat, Patrick Chastellan, Isabelle Coelho, Kora Combres, Chantal Ginestoux, Veronique Giudicelli, Denys Chaume, Gerard Lefranc
2005 In Silico Biology  
IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins  ...  IMGT-Choreography will further increase the IMGT leadership in immunogenetics and immunoinformatics for medical research (repertoire analysis of the IG antibody sites and of the TR recognition sites in  ...  ACKNOWLEDGEMENTS We are grateful to Mehdi Yousfi Monod, Joumana Jabado-Michaloud and Vincent Negre for helpful discussion.  ... 
pmid:15972004 fatcat:66kgcezv6zh5vmtfyuhma4ebeq

IMGT, the international ImMunoGeneTics database(R)

M.-P. Lefranc
2003 Nucleic Acids Research  
The international ImMunoGeneTics database 1 (IMGT) (http://imgt.cines.fr), is a high quality integrated information system specializing in Immunoglobulins (IG), T cell Receptors (TR) and Major Histocompatibility  ...  Complex (MHC) of human and other vertebrates, created in 1989, by the Laboratoire d'ImmunoGé né tique Molé culaire (LIGM), at  ...  ACKNOWLEDGEMENTS IMGT is funded by the European Union's 5th PCRDT programme (QLG2-2000-01287), the Centre National de la Recherche Scientifique (CNRS), the Ministère de l'Education Nationale et de la Recherche  ... 
doi:10.1093/nar/gkg085 pmid:12520009 pmcid:PMC165532 fatcat:kptcm56y5bfg7daxk3vlm5gvqi

Recovering probabilities for nucleotide trimming processes for T cell receptor TRA and TRG V-J junctions analyzed with IMGT tools

Kevin Bleakley, Marie-Paule Lefranc, Gérard Biau
2008 BMC Bioinformatics  
Nucleotides are trimmed from the ends of variable (V), diversity (D) and joining (J) genes during immunoglobulin (IG) and T cell receptor (TR) rearrangements in B cells and T cells of the immune system  ...  This trimming is followed by addition of nucleotides at random, forming the N regions (N for nucleotides) of the V-J and V-D-J junctions.  ...  We are grateful to Yan Wu for data analysis, Véronique Giudicelli, Xavier Brochet, François Ehrenmann and Patrice Duroux for their contribution to upgrading the IMGT/V-QUEST software.  ... 
doi:10.1186/1471-2105-9-408 pmid:18831754 pmcid:PMC2576266 fatcat:cblqhyyp6vh6jhnr7rjlyvnwsy

IG and TR single chain fragment variable (scFv) sequence analysis: a new advanced functionality of IMGT/V-QUEST and IMGT/HighV-QUEST

Véronique Giudicelli, Patrice Duroux, Sofia Kossida, Marie-Paule Lefranc
2017 BMC Immunology  
Immunoglobulins (IG) or antibodies and T cell receptors (TR) are managed and described in the IMGT® databases and tools at the level of receptor, chain and domain.  ...  It proceeds in five steps: search for a first closest V-REGION, full characterization of the first V-(D)-J-REGION, then search for a second V-REGION and full characterization of the second V-(D)-J-REGION  ...  Acknowledgements We thank Gisèle Clofent-Sanchez and Audrey Hemadou for scFv sequences samples and their implication in the development of the project.  ... 
doi:10.1186/s12865-017-0218-8 pmid:28651553 pmcid:PMC5485737 fatcat:vlkvfytryzh4ricc22dsukuxqe

IMGT standardization for statistical analyses of T cell receptor junctions: the TRAV-TRAJ example

Kevin Bleakley, Véronique Giudicelli, Yan Wu, Marie-Paule Lefranc, Gérard Biau
2006 In Silico Biology  
The diversity of immunoglobulin (IG) and T cell receptor (TR) chains depends on several mechanisms: combinatorial diversity, which is a consequence of the number of V, D and J genes and the N-REGION diversity  ...  We have chosen the human TRAV-TRAJ junctions as an example in order to characterize the required criteria for a standardized analysis of the IG and TR V-J and V-D-J junctions, based on the IMGT-ONTOLOGY  ...  We are grateful to Xavier Brochet for his contribution to the improvement of the IMGT/V-QUEST software. We thank Gérard Lefranc for fruitful discussion and the IMGT team for its constant  ... 
pmid:17518765 fatcat:p4hdldbd3bbvdoehszed57rfve

IMGT/HIGHV-QUEST: THE IMGT® WEB PORTAL FOR IMMUNOGLOBULIN (IG) OR ANTIBODY AND T CELL RECEPTOR (TR) ANALYSIS FROM NGS HIGH THROUGHPUT AND DEEP SEQUENCING

2012 Immunome Research  
the V-(D)-J junctions and, for IG, somatic hypermutations.  ...  The number of antigen receptors, immunoglobulins (IG) or antibodies and T cell receptors (TR) of the adaptive immune response in vertebrates with jaws is almost unlimited (2.10 12 per individual in humans  ...  ACKNOWLEDGEMENTS We thank Gérard Lefranc for helpful comments. We are grateful to the IMGT® team for its constant motivation and expertise.  ... 
doi:10.4172/1745-7580.1000056 fatcat:fr36mu5qibgprh3vulxco56tge

IMGT-ONTOLOGY and IMGT databases, tools and Web resources for immunogenetics and immunoinformatics

Marie-Paule Lefranc
2004 Molecular Immunology  
analysis (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/PhyloGene, IMGT/Allele-Align), for genome analysis (IMGT/GeneSearch, IMGT/GeneView, IMGT/LocusView) and for 3D structure analysis (IMGT/StructuralQuery  ...  The international ImMunoGeneTics information system ® (IMGT; http://imgt.cines.fr), is a high quality integrated information system specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility  ...  Acknowledgements I am deeply grateful to the IMGT team for its hard work, expertise, constant motivation and enthusiasm.  ... 
doi:10.1016/j.molimm.2003.09.006 pmid:14644091 fatcat:3pcslonq4zawjnygo5skyiixpu

IMGT, the international ImMunoGeneTics database: a high-quality information system for comparative immunogenetics and immunology

Marie-Paule Lefranc
2002 Developmental and Comparative Immunology  
IMGT Index, and interactive tools (IMGT/V-QUEST, IMGT/JunctionAnalysis).  ...  IMGT, the international ImMunoGeneTics database (http://imgt.cines.fr), is a high quality integrated information system specializing in Immunoglobulins (IG), T cell Receptors (TR) and Major Histocompatibility  ...  Acknowledgments I thank Véronique Giudicelli, Denys Chaume and Gérard Lefranc for helpful discussion, Chantal Ginestoux for the figure and Nora Bonnet for typing the manuscript.  ... 
doi:10.1016/s0145-305x(02)00026-5 pmid:12206833 fatcat:ko5uic5fbbeoliu76o7l6clani

IMGT, the international ImMunoGeneTics information system: a standardized approach for immunogenetics and immunoinformatics

Marie-Paule Lefranc
2005 Immunome Research  
IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins  ...  IMGT is the international reference in immunogenetics and immunoinformatics for medical research (repertoire analysis of the IG antibody sites and of the TR recognition sites in autoimmune and infectious  ...  IMGT/JunctionAnalysis IMGT/JunctionAnalysis [11] is a tool, complementary to IMGT/V-QUEST, which provides a thorough analysis of the V-J and V-D-J junction of IG and TR rearranged genes.  ... 
doi:10.1186/1745-7580-1-3 pmid:16305737 pmcid:PMC1312312 fatcat:6hkqzcde6bcvjgvgeosbpel2k4

IMGT, the international ImMunoGeneTics information system(R)

M.-P. Lefranc
2004 Nucleic Acids Research  
, France, is a high-quality integrated knowledge resource specializing in the immunoglobulins (IGs), T cell receptors (TRs), major histocompatibility complex (MHC) of human and other vertebrates, and related  ...  IMGT tools are particularly useful for the analysis of the IG and TR repertoires in normal physiological and pathological situations.  ...  IMGT/JunctionAnalysis (16) is a tool, complementary to IMGT/V-QUEST, which provides a thorough analysis of the V-J and V-D-J junctions that confer the antigen receptor specificity to IG and TR rearranged  ... 
doi:10.1093/nar/gki065 pmid:15608269 pmcid:PMC540019 fatcat:7bh7zpn4lna43ehvgy5avusgvu
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