This folder contains the IMGT reference directory [1,2,3] used by IMGT/V-QUEST [4,5,6], IMGT/JunctionAnalysis [7] and IMGT/HighV-QUEST [8,9,10] for the identification of IMGT gene and allele in IG and TR rearranged sequences. The IMGT reference directory in FASTA format is constituted by sets of immunoglobulin (IG) or T cell receptor (TR) sequences which are isolated from the IMGT reference sequences. - By definition, the IMGT reference directory sets contain one sequence for each allele. Allele names of these sequences are shown in red in Alignments of alleles. - In the V-REGION sets, IMGT gaps have been introduced according to the IMGT unique numbering [12][13][14]. - Gene names with provisional nomenclature (with a letter S) correspond to genes not yet assigned to genomic mapped genes. They correspond to insertion/deletion polymorphism in different strains or to mutated genes. - NL: Not Localized. IMGT IG and TR genes [15] are managed in the IMGT gene database IMGT/GENE-DB (http://www.imgt.org/genedb/) [11] and in IMGT Web resources (http://www.imgt.org/IMGTrepertoire/). The IMGT FASTA header of nucleotide IMGT reference sequences contains 15 fields separated by '|’: 1. IMGT/LIGM-DB accession number(s) 2. IMGT gene and allele name 3. species 4. IMGT allele functionality 5. exon(s), region name(s), or extracted label(s) 6. start and end positions in the IMGT/LIGM-DB accession number(s) 7. number of nucleotides in the IMGT/LIGM-DB accession number(s) 8. codon start, or 'NR' (not relevant) for non coding labels 9. +n: number of nucleotides (nt) added in 5' compared to the corresponding label extracted from IMGT/LIGM-DB 10. +n or -n: number of nucleotides (nt) added or removed in 3' compared to the corresponding label extracted from IMGT/LIGM-DB 11. +n, -n, and/or nS: number of added, deleted, and/or substituted nucleotides to correct sequencing errors, or 'not corrected' if non corrected sequencing errors 12. number of amino acids (AA): this field indicates that the sequence is in amino acids 13. number of characters in the sequence: nt (or AA)+IMGT gaps=total 14. partial (if it is) 15. reverse complementary (if it is) For genes from species and locus which are not yet managed in IMGT/GENE-DB, the FASTA header comprises 5 fields separated by "|": - the IMGT accession number - the IMGT gene name and allele - the species - the gene and alleles functionality - the core REGION (V-REGION, D-REGION or J-REGION) plus 10 empty fields IMGT/V-QUEST reference directory sets: - The IMGT/V-QUEST reference directory sets are constituted by sets of sequences which contain the V-REGION, D-REGION and J-REGION alleles, isolated from the Functional (F), ORF and in-frame pseudogene (P) allele IMGT reference sequences. By definition, these sets contain one sequence for each allele. Allele names of these sequences are shown in red in Alignments of alleles. - The IMGT/V-QUEST reference directory sets also include orphons. - IMGT/V-QUEST reference directory sets are listed per species and per IMGT group. - IMGT/V-QUEST reference directory sets are provided in FASTA files. References: [1] Lefranc M.-P. and Lefranc G. The Immunoglobulin FactsBook (2001), Academic Press, London, UK (458 pages) [2] Lefranc M.-P. and Lefranc G. The T cell receptor FactsBook (2001), Academic Press, London, UK (398 pages) [3] Lefranc M.-P. , et al. IMGT®, the international ImMunoGeneTics information system® 25 years on. Nucleic Acids Res., 37, 1006-1012 (2015). PMID:18978023 LIGM:349 [4] Giudicelli, V. et al. Nucl. Acids Res. 32, W435-440 (2004) PMID: 15215425 LIGM:287 [5] Brochet, X. et al. Nucl. Acids Res. 36, W503-508 (2008). PMID:18503082 LIGM:344 [6] Giudicelli V., et al., BMC Immunol. 2017 Jun 26;18(1):35. doi: 10.1186/s12865-017-0218-8. PMID: 28651553 Free PMC Article LIGM: 468 [7] Yousfi Monod, M. et al. Bioinformatics , 20, i379-i385 (2004) PMID: 15262823 LIGM:289 [8] Alamyar, E. et al., Immunome Res. 8:1:2. (2012) doi:10.4172/1745-7580.1000056. LIGM:400 [9] Alamyar E., et al., Methods Mol. Biol. 882:569-604 (2012). PMID:22665256 LIGM:404 [10] Giudicelli V., et al., Autoimmun Infec Dis. 1(1) (2015). doi: 10.16966/aidoa.103. Free Article LIGM:448 [11] Giudicelli V., Chaume D. and Lefranc M.-P. Nucl. Acids Res., 33, D256-D261 (2005). PMID: 15608191 LIGM:292 [12] Lefranc, M.-P. Methods Mol. Biol. 248, 27-49 (2004) PMID: 14970490 LIGM:277 [13] Lefranc, M.-P. Current Protocols in Immunology pp. A1W.1-A.1W.15 (2006) PMID: 18432961 LIGM:311 [14] Lefranc, M.-P. et al., Dev. Comp. Immunol., 27, 55-77 (2003) PMID: 12477501 LIGM:268 [15] Lefranc, M.-P., Immunoglobulin (IG) and T cell receptor genes (TR): IMGT® and the birth and rise of immunoinformatics. Front Immunol. 2014 Feb 05;5:22. doi: 10.3389/fimmu.2014.00022. Open access. PMID: 24600447 LIGM:429 Software material and data coming from IMGT server may be used for academic research only, provided that it is referred to IMGT, and cited as "IMGT, the international ImMunoGeneTics information system http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)." Reference to cite : - Lefranc M-P, Giudicelli V, Duroux P, Jabado-Michaloud J, Folch G, Aouinti S, Carillon E, Duvergey H, Houles A, Paysan-Lafosse T, Hadi-Saljoqi S, Sasorith S, Lefranc G, Kossida S. IMGT®, the international ImMunoGeneTics information system® 25 years on. Nucleic Acids Res. 2015 Jan;43(Database issue):D413-22. doi: 10.1093/nar/gku1056. Epub 2014 Nov 5 Free article. PMID: 25378316 LIGM:441 - Lefranc, M.-P., Immunoglobulin (IG) and T cell receptor genes (TR): IMGT® and the birth and rise of immunoinformatics. Front Immunol. 2014 Feb 05;5:22. doi: 10.3389/fimmu.2014.00022. Open access. PMID: 24600447 LIGM:429 For any other use please contact Marie-Paule Lefranc Marie-Paule.Lefranc@igh.cnrs.fr and Sofia Kossida Sofia.Kossida@igh.cnrs.fr. IMGT founder and Executive Director Emeritus: Marie-Paule Lefranc Marie-Paule.Lefranc@igh.cnrs.fr IMGT Director: Sofia Kossida Sofia.Kossida@igh.cnrs.fr Bioinformatics manager: Veronique Giudicelli Veronique.Giudicelli@igh.cnrs.fr Computer manager: Patrice Duroux Patrice.Duroux@igh.cnrs.fr Copyright 1995-2019 IMGT®, the international ImMunoGeneTics information system®.