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IMGT/Automat: the strategy for the annotation of human and mouse cDNA nucleotide sequences of IG and TR

Géraldine Folch¹, Joumana Jabado-Michaloud¹, Fatena Bellahcene¹, Laetitia Regnier¹, Véronique Giudicelli¹ & Marie-Paule Lefranc¹

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1. IMGT

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Document Type:

Poster

Date:

Received 23 April 2009 13:49 UTC; Posted 23 April 2009

Subjects:

Genetics & Genomics, Immunology, Bioinformatics

Tags:

• TR annotation
• T cell receptors
• gene rearrangement
• cDNA database
• tool
• Immunoglobulin
• IMGT
• annotation
• cDNA
• immunogenetics
• immunology
• database

Abstract:

The cDNA sequences of immunoglobulins (IG) and T cell receptors (TR) represent more than one half of the sequences in the IMGT^® nucleotide database IMGT/LIGM-DB¹ and 75% of them are from human and mouse. A few cDNA are germline but the great majority results from a V-D-J or V-J gene rearrangement, spliced to a C gene. The IG and TR genes have been studied extensively in IMGT^® (http://www.imgt.org) ², which allowed to set up their nomenclature and the corresponding germline reference sequences. These standardized reference directory sets (one for each group of each locus) and the IMGT-ONTOLOGY axioms and derived concepts³ are the key elements indispensable to perform the annotation of IG and TR cDNA sequences. A Java program, IMGT/Automat⁴, was developed by IMGT^®, to automatically annotate the IG and TR cDNA sequences and to produce a totally automatic and complete annotation. More than 9,000 human and mouse cDNA have already been successfully automatically annotated. The quality of the cDNA automatic annotation is equivalent to the quality of the annotation achieved by a human expert. The IMGT^® strategy is currently the only way, in the field of immunogenetics, to guarantee the annotation quality and the management of an always increasing number of IG and TR cDNA nucleotide sequences.

Collection:

3rd International Biocuration Conference

Presented at:

3rd International Biocuration Conference, 16 April 2009

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License:

This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Folch, Géraldine, Jabado-Michaloud, Joumana, Bellahcene, Fatena, Regnier, Laetitia, Giudicelli, Véronique, and Lefranc, Marie-Paule. IMGT/Automat: the strategy for the annotation of human and mouse cDNA nucleotide sequences of IG and TR. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3159.1> (2009)

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