IMGT/V-QUEST programme versions

Citing IMGT/V-QUEST: Brochet, X. et al., Nucl. Acids Res. 36, W503-508 (2008). PMID: 18503082 Giudicelli, V., Brochet, X., Lefranc, M.-P., Cold Spring Harb Protoc. 2011 Jun 1;2011(6). pii: pdb.prot5633. doi: 10.1101/pdb.prot5633. PMID: 21632778 Abstract also in IMGT booklet with generous provision from Cold Spring Harbor (CSH) Protocols (high res) (lower res)

IMGT/V-QUEST programme version: 3.2.23 (6 January 2012) - IMGT/V-QUEST reference directory release: 201201-5 (6 January 2012)

• Version 3.2.23 (6th of January 2012)
  • Addition of a consistency control for the end position of the J-GENE and allele in absence of JUNCTION.

• Version 3.2.22 (16th of December 2011)
  • Addition of a consistency control for the end position of the J-GENE and allele and the delimitation of the JUNCTION.

• Version 3.2.21 (8th of November 2011)
  • Improvement of the analysis of the junction for TRAV/DV-TRDJ and TRAV/DV-TRAJ sequences.

• Version 3.2.20 (26th of July 2011)
  • In Summary table of Synthesis view: update of the display of the "J-GENE and allele" when there are several solutions.

  • In alignments of Synthesis view: update of the display of the functionality that follows the genes and alleles names (see the section IMGT/V-QUEST reference directory sets of the IMGT/V-QUEST Documentation).

• Version 3.2.19 (27th of June 2011)
  • Update of the display of the IMGT gene and allele names: gene and allele names are preceded by the short name of the species (encoded on 6 characters, for example Homsap for Homo sapiens or Musmus for Mus musculus) and they are followed by the gene and allele functionality.

  • In Advanced parameters, Parameters for IMGT/JunctionAnalysis: the modification of the default numbers of mutations allowed in the 3'V-REGION, D-REGION, and /or 5'J-REGION by the user is taken into account even in case of unmutated IG sequences.

  • In Detailed View, Annotation by IMGT/Automat: the N-AND-D-REGION has been changed to (N-D)-REGION and N-AND-D-J-REGION to (N-D)-J-REGION.

  • In Excel file: addition of a column for (N-D)-J-REGION in the nt-sequence sheet.

  • In Excel file: update of the display of the functionality field in the Junction sheet (correction of a bug for sequences with functionality "unknown").

  • Update of "V-REGION protein display" of Detailed View, of "V-REGION protein display", "V-REGION protein display (with AA class colors)" and "V-REGION protein display (only AA changes displayed)" of Synthesis View in case of additional positions in the IMGT numbering.

• Version 3.2.18 (29th of March 2011)
  • Update of the display of the IMGT/V-QUEST Welcome page and of the IMGT/V-QUEST Search pages.

• Version 3.2.17 (29th of November 2010)
  • Addition of a control for extremely partial sequences in 5': no results are provided for sequences with partial CDR3 in 5' .
  • Addition of the Receptor type or locus (IG or TR) in the Parameters sheet of the Excel file.

• Version 3.2.16 (13th of September 2010)
  • Addition of a control on the sequence length: no results are provided for sequences shorter than 9 nucleotides.

• Version 3.2.15 (28th of July 2010)
  • Order of the options and the results in "A. Detailed View"
    Owing to the coming soon IMGT/HighV-QUEST, the order of the options and the results in "Detailed View" has been changed as follows:
    - 12. Sequences of V-, V-J- or V-D-J- REGION ('nt' and 'AA') with gaps in FASTA and access to IMGT/PhyloGene for V-REGION ('nt')
    - 13. Annotation by IMGT/Automat
    - 14. IMGT Collier de Perles

  • Addition of a third option for Selection for results: "C. Excel file"
    Users are allowed to select the sheets to be included in the Excel file :
    
    1. Summary (always selected)
    2. IMGT-gapped-nt-sequences
    3. nt-sequences
    4. IMGT-gapped-AA-sequences
    5. AA-sequences
    6. Junction
    7. V-REGION-mutation-and-AA-change-table
    8. V-REGION-nt-mutation-statistics
    9. V-REGION-AA-change-statistics
    10. V-REGION-mutation-hot-spots
    11. Parameters (always selected)
    Note that the "Summary" and "Parameters" are always included.

  • In results of "A. Detailed view" and "B. Synthesis view", HTML and Text output: the top of the page includes the IMGT/V-QUEST programme version and IMGT/V-QUEST reference directory releases.

  • In results of "A. Detailed view", option "Search for insertions and deletions", text output: In case of detected insertions in the submitted sequence, the inserted nucleotides are shown as capital letters in the FASTA sequence as capital letters in the FASTA sequence (as for HTML and Excel output).

  • In results of "A. Detailed view", Result summary: the last line of the table includes:
    
    • the FR-IMGT lengths
    • the CDR-IMGT lengths
    • the amino acid JUNCTION

IMGT/V-QUEST Search page
IMGT/V-QUEST Documentation

Contact IMGT/V-QUEST, Montpellier, France : Véronique Giudicelli (Veronique.Giudicelli@igh.cnrs.fr) and Marie-Paule Lefranc (Marie-Paule.Lefranc@igh.cnrs.fr)

Created: 07/07/2010
Last updated: 28/07/2010
Authors: Véronique Giudicelli and Marie-Paule Lefranc.
Marie-Paule.Lefranc@igh.cnrs.fr

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 (Initiator and coordinator: Marie-Paule Lefranc, Montpellier, France)." References to cite: Lefranc, M.-P. et al., Nucleic Acids Research, 27, 209-212 (1999) Cover of NAR; Ruiz, M. et al., Nucleic Acids Research, 28, 219-221 (2000); Lefranc, M.-P., Nucleic Acids Research, 29, 207-209 (2001), Lefranc, M.-P., Nucleic Acids Res., 31, 307-310 (2003) Full text; Lefranc, M.-P. et al., In Silico Biol., 5, 0006 (2004), Lefranc, M.-P. et al., Nucleic Acids Res., 33, D593-D597 (2005) Full text; Lefranc, M.-P. et al., Nucleic Acids Research 2009 37(Database issue): D1006-D1012; doi:10.1093/nar/gkn838 Full text.

For any other use please contact Marie-Paule Lefranc Marie-Paule.Lefranc@igh.cnrs.fr.

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