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The first concepts were defined as "relevant and fundamental criteria which are needed to characterize IG and TR data" (Giudicelli and Lefranc, 1999) . ... et al., 2006) IMGT/Automat, the IMGT® tool for the annotation of rearranged cDNA (Giudicelli et al., 2005a) implements corresponding labels and prototypes. ...doi:10.3389/fgene.2012.00079 pmid:22654892 pmcid:PMC3358611 fatcat:o7ny6ofyq5amjhko6z45wvbudq
The seq1 accession number is DQ100777 from the IMGT/LIGM-DB database (Giudicelli et al. 2006 ). ... By clicking on "Start", the analysis is done automatically with the default parameters Giudicelli and Lefranc 2008) . ...doi:10.1007/978-3-642-01147-4_2 fatcat:2l3ri26k2nbhbd7fuiwtgyesx4
.), IMGT® gene database (IMGT/GENE-DB) and IMGT reference directory sets of the IMGT® tools (IMGT/V-QUEST, IMGT/JunctionAnalysis and IMGT/DomainGapAlign).  Giudicelli, V. et al., Nucleic Acids Res., ... in vitro cDNA) mRNA (or in vitro cDNA) ).Duroux, P. et al., Biochimie, 90, 570-583 (2008). Giudicelli, V. and Lefranc, M.-P. ... The concepts of identification, classification, description and numerotation are particuraly used for the immunogenetic sequence annotation.  Giudicelli, V. and Lefranc, M. ...doi:10.1038/npre.2009.3165.1 fatcat:4dtmiolo45hsvhy5lwwdecgbyi
IMGT Ò , the international ImMunoGeneTics information system Ò (http://imgt.cines.fr), is the reference in immunogenetics and immunoinformatics. IMGT standardizes and manages the complex immunogenetic data which include the immunoglobulins (IG) or antibodies, the T cell receptors (TR), the major histocompatibility complex (MHC) and the related proteins of the immune system (RPI) which belong to the immunoglobulin superfamily (IgSF) and the MHC superfamily (MhcSF). The accuracy and consistencydoi:10.1016/j.biochi.2007.09.003 pmid:17949886 fatcat:epwhbxlop5fgddmsv2zaunirle
more »... IMGT data and the coherence between the different IMGT components (databases, tools and Web resources) are based on IMGT-ONTOLOGY, the first ontology for immunogenetics and immunoinformatics. IMGT-ONTOLOGY manages the immunogenetics knowledge through diverse facets relying on seven axioms,
Identifying and annotating Immunoglobulins (IG), T cell receptors (TR) genes of jawed vertebrate species effectively and precisely is still an arduous task, essentially due to the continuous avalanche of large genomic sequences produced by NGS technologies. In this study, to predict the L-PART1 exon (the first exon of IG and TR variable V-GENE), different Deep Neural Network-based models (DNN, CNN, RNN, CNN-RNN) were trained in a supervised manner, which automatically learn features fromdoi:10.14806/ej.26.a.957 fatcat:ewmjh5rf2va6jnnd3wf33sa7da
more »... ed IG and TR genes. Those models will then be used to predict the L-PART1 exon within newly given sequences. Correct detection of this component would dramatically increase the chances to find the subsequent components constituting the V-GENE of the IG and TR. Sequence data were extracted from IMGT/ LIGM-DB, the IMGT® (Lefranc et al., 2015) nucleotides database: around 2756 L-PART1 of 354 species tagged as positive samples, negative samples were generated with different noise strategies. The final training datasets were formed by shuffling a portion of positive and negative samples. The majority of the trained models showed promising results. However, further studies are needed to investigate the possibility of predicting and locating all the components within the V-GENE of IG and TR.
Nowadays, Deep Learning is taking the world by a storm, known as a technology that makes use of Artificial Neural Networks to automatically extrapolate knowledge from a training data set, then uses this knowledge to give predictions for unseen samples. This data driven paradigm gained a widespread adoption in many disciplines, from handwriting recognition, driving an autonomous car to cracking the 50-year-old protein folding problem. With this review, we shed some light on the concepts of Deepdoi:10.14806/ej.27.0.990 fatcat:uozmbvgc7fbdfltecd2jczbsze
more »... earning and provide some visualizations, skim over the different architectures such as Deep Neural Network (DNN), Convolutional Neural Network (CNN), Recurrent Neural Network (RNN) and touch upon the modern architectures such as Transformers and BERT. We also provide various examples targeting the genomics field, reference utilities, libraries useful for newcomers and disseminate our feedback.
In Silico Biology
IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), was created in 1989 at Montpellier, France. 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 of the immune system (RPI) which belong to the immunoglobulin superfamily (IgSF) and MHC superfamily (MhcSF). IMGT provides a common access to standardized data frompmid:15972004 fatcat:66kgcezv6zh5vmtfyuhma4ebeq
more »... ome, proteome, genetics and three-dimensional structures. The accuracy and the consistency of IMGT data are based on IMGT-ONTOLOGY, a semantic specification of terms to be used in immunogenetics and immunoinformatics. IMGT-ONTOLOGY has been formalized using XML Schema (IMGT-ML) for interoperability with other information systems. We are developing Web services to automatically query IMGT databases and tools. This is the first step towards IMGT-Choreography which will trigger and coordinate dynamic interactions between IMGT Web services to process complex significant biological and clinical requests. 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 autoimmune and infectious diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research (IG and TR repertoires in farm and wild life species), genome diversity and genome evolution studies of the adaptive immune responses, biotechnology related to antibody engineering (single chain Fragment variable (scFv), phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (detection and follow up of residual diseases) and therapeutical approaches (grafts, immunotherapy, vaccinology). IMGT is freely available at http://imgt.cines.fr.
Pallarès/Frippiat/Giudicelli/Lefranc Table 5 ExpClin Immunogenet 1998;15:8-18 ...doi:10.1159/000019054 pmid:9619396 fatcat:3sick2ednvfkticoj2ykafivs4
., 2010) and analysed rearranged sequences (Giudicelli et al., 2004) . ... For this part, as for the bioinformatics topic, the pupils explored two specialised databases, IMGT/LIGM-DB (Giudicelli et al., 2006) and IMGT/GENE-DB (Giudicelli et al., 2005) . ...doi:10.14806/ej.25.1.926 fatcat:ckoawtdrdraftkedy4zr74ggti
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, which creates an extensive and clonal somatic diversity at the V-J and V-D-J junctions. For the IG, the diversity is further increased by somatic hypermutations. The number of different junctions per chain and per individual is estimated to be 10(12). We have chosen the human TRAV-TRAJpmid:17518765 fatcat:p4hdldbd3bbvdoehszed57rfve
more »... ctions 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 concepts, and to serve as a first IMGT junction reference set (IMGT, http://imgt.cines.fr). We performed a thorough statistical analysis of 212 human rearranged TRAV-TRAJ sequences, which were aligned and analysed by the integrated IMGT/V-QUEST software, which includes IMGT/JunctionAnalysis, then manually expert-verified. Furthermore, we compared these 212 sequences with 37 other human TRAV-TRAJ junction sequences for which some particularities (potential sequence polymorphisms, sequencing errors, etc.) did not allow IMGT/JunctionAnalysis to provide the correct biological results, according to expert verification. Using statistical learning, we constructed an automatic warning system to predict if new, automatically analysed TRAV-TRAJ sequences should be manually re-checked. We estimated the robustness of this automatic warning system.
 Giudicelli V. et al. Nucleic Acids Res., 33, D256-261 (2005). ... /www.imgt.org IMGT/GENE-DB: genomic reference sequences for human and mouse IG and TR genes and allelesFatena Bellahcene, Géraldine Folch, Joumana Jabado-Michaloud, Chantal Ginestoux, Patrice Duroux, Véronique ...doi:10.1038/npre.2009.3158.1 fatcat:wtm3zo33krcnpm2rgdlygz2soa
The adaptive immune system, along with the innate immune system, are the two main biological processes that protect an organism from pathogens. The adaptive immune system is characterized by the specificity and extreme diversity of its antigen receptors. These antigen receptors are the immunoglobulins (IG) or antibodies of the B cells and the T cell receptors (TR) of the T cells. The IG are proteins that have a dual role in immunity: they recognize antigens and trigger elimination mechanisms,doi:10.3390/vaccines10030394 pmid:35335026 pmcid:PMC8950363 fatcat:3bg6ekx37zczfakexzavzznpgq
more »... rid the body of foreign cells. The synthesis of the immunoglobulin heavy and light chains requires gene rearrangements at the DNA level in the IGH, IGK, and IGL loci. The rhesus monkey (Macaca mulatta) is one of the most widely used nonhuman primate species in biomedical research. In this manuscript, we provide a thorough analysis of the three IG loci of the Mmul_10 assembly of rhesus monkey, integrating IMGT previously existing data. Detailed characterization of IG genes includes their localization and position in the loci, the determination of the allele functionality, and the description of the regulatory elements of their promoters as well as the sequences of the conventional recombination signals (RS). This complete annotation of the genomic IG loci of Mmul_10 assembly and the highly detailed IG gene characterization could be used as a model, in additional rhesus monkey assemblies, for the analysis of the IG allelic polymorphism and structural variation, which have been described in rhesus monkeys.
Nucleic Acids Res., 34, D781-784 (2006) .  Giudicelli V. et al. Stud. Health Technol. Inform., 116, 3-8 ( 2005) .  Brochet X. et al. ... 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.  Giudicelli ...doi:10.1038/npre.2009.3159.1 fatcat:dx723jzvmnachledtnm6kwn2ia
The adaptive immune response provides the vertebrate immune system with the ability to recognize and remember specific pathogens to generate immunity, and mount stronger attacks each time the pathogen is encountered. T cell receptors are the antigen receptors of the adaptive immune response expressed by T cells, which specifically recognize processed antigens, presented as peptides by the highly polymorphic major histocompatibility (MH) proteins. T cell receptors (TR) are divided into twodoi:10.3390/genes12010030 pmid:33379283 pmcid:PMC7824213 fatcat:itbwg2shx5fmfhche6il3cuo34
more »... , αβ and γδ, which express distinct TR containing either α and β, or γ and δ chains, respectively. The TRα locus (TRA) and TRδ locus (TRD) of bovine (Bos taurus) and the sheep (Ovis aries) have recently been described and annotated by IMGT® biocurators. The aim of the present study is to present the results of the biocuration and to compare the genes of the TRA/TRD loci among these ruminant species based on the Homo sapiens repertoire. The comparative analysis shows similarities but also differences, including the fact that these two species have a TRA/TRD locus about three times larger than that of humans and therefore have many more genes which may demonstrate duplications and/or deletions during evolution.
Giudicelli, P Duroux, S Kossida, M.P. Lefranc To cite this version: V. Giudicelli, P Duroux, S Kossida, M.P. Lefranc. ...doi:10.1186/s12865-017-0218-8 pmid:28651553 pmcid:PMC5485737 fatcat:vlkvfytryzh4ricc22dsukuxqe
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