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

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-DB^1^ 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":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 concepts^3^ are the key elements indispensable to perform the annotation of IG and TR cDNA sequences. A Java program, IMGT/Automat^4^, 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.

IMGT® Biocuration and Comparative Study of the T Cell Receptor Beta Locus of Veterinary Species Based on Homo sapiens TRB

“…The biocuration has been performed manually assisted by internally developed tools [IMGT/LIGMotif (18), NtiToVald and IMGT/Automat (19)] based on the IMGT-ONTOLOGY axioms and concepts: "IDENTIFICATION, " "DESCRIPTION, " "CLASSIFICATION, " "NUMEROTATION, " "LOCALIZATION, " "ORIENTATION, " and "OBTENTION" (20). IMGT-ONTOLOGY includes the controlled vocabulary and annotation rules which are indispensable to ensure accuracy, consistency and coherence.…”

IMGT® Biocuration and Analysis of the Rhesus Monkey IG Loci

“…The biocuration was performed manually assisted by internally developed tools IMGT/LIGMotif [ 32 ], NtiToVald [ 33 ] and IMGT/Automat [ 33 ] based on the IMGT-ONTOLOGY axioms and concepts: “IDENTIFICATION”, “DESCRIPTION”, “CLASSIFICATION”, “NUMEROTATION”, “LOCALIZATION”, “ORIENTATION”, and “OBTENTION” [ 34 ]. IMGT-ONTOLOGY includes the controlled vocabulary and annotation rules which are indispensable to ensure accuracy and consistency.…”