IMGT®, the international ImMunoGeneTics information system®

Sequence submission for IMGT/LIGM-DB

Data flow and IMGT/LIGM-DB annotations

The main source of data for IMGT/LIGM-DB is EMBL which shares data with the other two generalist databases GenBank and DDBJ. IMGT/LIGM-DB contains the IG and TR sequences which are allowed by the authors to be made public. IMGT/LIGM-DB sequence data are identified by the EMBL/GenBank/DDBJ accession number.

Immunoglobulin (IG) and T cell receptor (TR) sequences of all vertebrates should be submitted to EMBL-Bank ENA (Webin), GenBank (BankIt) or DDBJ.

For submission of new V genes and alleles, new D genes and alleles, new J genes and alleles and new C genes and alleles, see the recommendations of IMGT-NC

Authors are encouraged to check their sequences, if appropriate, with IMGT/V-QUEST before submitting them to EMBL, GenBank or DDBJ.

LIGM retrieves by FTP IG and TR sequences from EBI, the European Bioinformatics Institute. After control by LIGM curators, data are scanned to store sequences, bibliographical references and taxonomic data, and standardized IMGT/LIGM-DB keywords are assigned to all entries. Based on expert analysis, specific detailed annotations are added to the IMGT/LIGM-DB flat files, according to the IMGT Scientific chart rules, based on IMGT-ONTOLOGY.

List of the rescued IG and TR sequences by LIGM

Since August 1996, the IMGT/LIGM-DB content follows the EMBL one for the IG and TR, with the following advantages: IMGT/LIGM-DB does not contain sequences which have previously been wrongly assigned to IG and TR; conversely, IMGT/LIGM-DB contains IG and TR entries which have disappeared from the generalist databases.

• in 1996, the L36092 accession number which encompasses the complete human TRB locus is present in IMGT/LIGM-DB (it was deleted from EMBL/GeneBank/DDBJ due to its too large size (684,973 bp) up to 2003).
• in 1999, IMGT/LIGM-DB detected the disappearance of 20 IG and TR sequences which inadvertently had been lost by GenBank, and allowed the recuperation of these sequences in the generalist databases:

  List of the accession numbers of the 20 IG and TR sequences for which the IMGT team noticed the disappearance from the GenBank release, in February 2000 (e-mail from Marie-Paule Lefranc to Jim Ostell, on the 11/02/2000). These sequences were also deleted from EMBL and DDBJ.

  • J00221
  • J00222
  • J03617
  • K01316
  • K01317
  • K01318
  • K01319
  • M17576
  • S42416
  • S42425
  • S59750
  • S59761
  • S59762
  • S59765
  • S59766
  • S59769
  • S64880
  • S67028
  • S70116
  • Z75464

  Except for Z75464, which was rightly deleted, the flat files of the other sequences were reintroduced in GenBank and in EMBL/DDBJ in March-April 2000.