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IMGT Index

IMGT/GENE-DB

Is it possible to retrieve flanking sequence at the 5' and/or 3' ends of IMGT labels that describe IMGT/GENE-DB annotated sequences?
Yes, flanking sequences at the 5' and/or 3' ends of the IMGT labels can be retrieved, in FASTA format, by querying the IMGT/GENE-DB entry section, "Choose your display > IMGT label extraction from IMGT/LIGM-DB reference sequences". For more information: IMGT label extraction from IMGT/LIGM-DB reference sequences.
How can I retrieve the V leader sequences from IMGT reference sequences?
Step 1: Make your selection (species, group, functionality) in IMGT/GENE-DB (access from http://www.imgt.org). For a selection "Homo sapiens", "IGHV" and "functional", the results of your search will be, for example:
Gene-DB result 1

Step 2: Select all genes (click in box at the bottom of the list of resulting genes) and in the "Choose your display" "IMGT label extraction from IMGT/LIGM-DB reference sequences" section, click on "Choose label(s) for extraction" and select the IMGT label "L-PART1+L-PART2" (L-PART1 and L-PART2 being shown as artificially spliced in that query).
Gene-DB result 2
How to obtain from IMGT/GENE-DB complete sequences of a constant gene, or of a group of C genes?
  1. To get the complete amino acid sequence (artificially spliced) of a reference constant gene, the query is 13.2
    • http://www.imgt.org/genedb/GENElect?query=13.2+Genesymbol&species=Species
      with for Genesymbol, the gene name (for instance IGHG1), and for Species, the latin name of the species (for instance Homo+sapiens) http://www.imgt.org/genedb/GENElect?query=13.2+IGHG1&species=Homo+sapiens
  2. To get the artificially spliced nucleotide sequence of that gene, the query is 13.1
  3. To get the complete amino acid sequence (artificially spliced) of reference constant genes of a group, the query is 14.2
    • http://www.imgt.org/genedb/GENElect?query=14.2+Group&species=Species
      with for Group, the group name (for instance IGHC), and for Species, the latin name of the species (for instance Homo+sapiens) http://www.imgt.org/genedb/GENElect?query=14.2+IGHC&species=Homo+sapiens
  4. To get the artificially spliced nucleotide sequence of that group, the query is 14.1
The information on the direct links are available at: http://www.imgt.org/genedb/directlinks
You can access that page at the bottom of the IMGT/GENE-DB Query page.
How to download the sequences of the available IG or TR genes of a given group of a given species, for example Homo sapiens IGHV, from IMGT/GENE-DB?
For the download of sequences, you may query the database:
in the IMGT/GENE-DB Query page, IDENTIFICATION: Species= Homo sapiens, CLASSIFICATION: IMGT group= IGHV.
At the bottom of the 'RESULTS OF YOUR SEARCH PAGE', click on "Select all genes", and in the section "Choose your display" (see http://www.imgt.org/genedb/doc#h2_62) select one of the options of "IMGT/GENE-DB allele reference sequences in FASTA format".

An alternative is to use an URL with format described in the direct links (http://www.imgt.org/genedb/directlinks), for example:
http://www.imgt.org/genedb/GENElect?query=7.2+IGHV&species=Homo+sapiens
How to retrieve sequences of the alleles of the human constant genes?
You can retrieve nucleotide and amino acid sequences of the alleles of a given gene in IMGT/GENE-DB (http://www.imgt.org/genedb/), from the table 'IMGT/GENE-DB reference sequences (in FASTA format)' displayed in the 'IMGT/GENE entry' page resulting from the query (for instance, Homo sapiens IGHG1).
You can retrieve nucleotide or amino acid sequences for a given gene (e.g., IGHG1 gene) or for genes of a group (e.g., IGHC group) of a given species (e.g., Homo sapiens), using the IMGT/GENE-DB direct links (http://www.imgt.org/genedb/directlinks).
Alleles can be compared visually in 'Alignments of alleles' (http://www.imgt.org/IMGTrepertoire/Proteins/index.php#B) in IMGT Repertoire.