IMGT/V-QUEST upgrades and versions anterior to July 2010

IMGT/V-QUEST upgrades and versions anterior to July 2010

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

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3rd of March 2010 (Version 3.2.14)
- Programme upgrade :
  - Improvement of the Excel file implementation.

26th of February 2010 (Version 3.2.13)
- Data upgrade :
  - Update of the IMGT/V-QUEST reference sequences for : Oryctolagus cuniculus IGHV1S35*01, Oryctolagus cuniculus IGHV1S43*01, Oryctolagus cuniculus IGHV1S44*01, Oryctolagus cuniculus IGHV1S45*01, Oryctolagus cuniculus IGHV1S46*01.

22th of February 2010 (Version 3.2.12)
- Data upgrade :
  - Addition of a new species: rabbit (Oryctolagus cuniculus):
  - 48 IGHV genes and alleles (40 F and 8 in-frame P)
  - 11 IGHD genes and alleles (10 F and 1 ORF)
  - 6 IGHJ genes and 11 alleles (F)
  - 66 IGKV genes and 68 alleles (66 F, 1 ORF, and 1 in-frame P)
  - 8 IGKJ genes and 19 alleles (8 F and 11 ORF)
  - Update of the human IGKV IMGT/V-QUEST reference sequences: addition of the orphon Homo sapiens IGKV1/ORY-1*01.
  - Update of the mouse IGKV IMGT/V-QUEST reference sequences: addition of Mus musculus IGKV10-94*07 and Mus musculus IGKV10-94*08.
  - Update of the trout IGHV IMGT/V-QUEST reference sequences: addition of Oncorhynchus mykiss IGHV5S10*01, Oncorhynchus mykiss IGHV2S2*02 and Oncorhynchus mykiss IGHV8S7*02.
  - Addition of the trout IGHD IMGT/V-QUEST reference sequences : 9 IGHD genes and alleles (F).
  - Addition of the trout IGHJ IMGT/V-QUEST reference sequences : 7 IGHJ genes and alleles (F).
  - Addition of the trout TRBV IMGT/V-QUEST reference sequences : 45 TRBV genes and alleles (39 F, 1 ORF and 5 in-frame P).
  - Addition of the trout TRBD IMGT/V-QUEST reference sequences : 1 TRBD gene and allele (F).
  - Addition of the trout TRBJ IMGT/V-QUEST reference sequences : 10 TRBJ genes and alleles (F).
- Programme upgrade :
  - In results of "A. Detailed view", option 12. IMGT Collier de Perles: update of the display "IMGT Collier de Perles (for a nb of sequences < 5)".

18th of December 2009 (Version 3.2.11)
- Data upgrade :
  - Update of the IMGT/V-QUEST reference sequences for : Homo sapiens IGHV1-45*02, Homo sapiens IGHV3-25*02, Homo sapiens IGHV3-48*03, Homo sapiens IGHV3-73*01.
  - Update of the IMGT/JunctionAnalysis: addition of Mus musculus TRAV7-1*01 and Mus musculus TRAV15D-2/DV6D-2*01.
- Programme upgrade :
  - Update of IMGT/JunctionAnalysis to deal with TRAV/TRDJ and TRDV/TRAJ rearranged sequences
  - Update the annotations by IMGT/Automat.

27th of October 2009 (Version 3.2.10)
- Data upgrade : Update of the rat IMGT reference directory set: Addition of 162 IGKV and 7 IGKJ genes and alleles.

5th of October 2009 (Version 3.2.9)
- In "Result summary" of "A. Detailed view" and in "Summary table" of "B. Synthesis view": evaluation of identity percentage when insertion(s) and/or deletion(s) have been detected (option "Search for insertions and deletions" of Advanced parameters). Between brackets are shown the percentage of identity and ratio considering each insertion or deletion as one mutational event. For each insertion or deletion, whatever its length, "1" is subtracted from the number of identical nucleotides.
- In "Results in Excel", in all sheets except "Parameters": addition of a column with the number of the analysed sequence.
- In "Results in Excel", "Summary" sheet: when the option "Search for insertions and deletions" of Advanced parameters is selected, addition of 2 columns "V-REGION identity % (with ins/del events)" and "V-REGION identity nt (with ins/del events)" that indicate the percentage of identity and ratio considering each insertion or deletion as one mutational event. For each insertion or deletion, whatever its length, "1" is subtracted from the number of identical nucleotides.
- Update of the evaluation of the number of amino acid changes at the end of the IMGT-CDR3.

1st of September 2009 (Version 3.2.8)
- In "Result summary" of "A. Detailed view" and in "Summary table" of "B. Synthesis view": addition of a note to the closest J-GENE and allele name when the JUNCTION has not been identified. It indicates that the results for J-GENE may be unreliable.
- Improvement of the control of the validity of the J-GENE and allele identification.

29th of July 2009 (Version 3.2.7)
- Correction of a bug for the determination of the JUNCTION.

28th of July 2009 (Version 3.2.6)
- In results of "A. Detailed view": Addition of the date of the analysis at the end of the page.
- In results of "B. Synthesis view": Addition of the date of the analysis at the end of the page.
- In "Results in Excel", "Parameters" sheet: Addition of the date of the analysis .
- In "Results in Excel", "IMGT-gapped-AA-sequences" sheet: update of the amino acid translation for sequences partial in 5'.

27th of July 2009 (Version 3.2.5)
- Improvement of the description of the JUNCTION for human, mouse and rat sequences with no W/FGXG conserved motif in the closest J gene.
- Improvement of the detection of P nucleotides in the JUNCTION (IMGT/JunctionAnalysis).
- In results of "A. Detailed view", option "12. IMGT Collier de Perles": Addition of CDR_length and FR_length.
- In results of "A. Detailed view", option "14. Annotation by IMGT/Automat": the qualifiers CDR_length et FR_length are associated to the V-D-J-REGION or V-J-REGION (or, if not possible, to the V-REGION).
- In results of "A. Detailed view", option "14. Annotation by IMGT/Automat": addition of the label N-AND-D-REGION.
- In "Results in Excel", "nt-sequences" sheet: addition of the label N-AND-D-REGION.

15th of June 2009 (Version 3.2.4)
- Update of the IMGT/V-QUEST query pages.
- "Results in text" output :elimination of HTML header and footer.
- "Results in text" for B. Synthesis view output: due to text format, hot spot positions are not more underlined in "1. Alignment for V-GENE", "2. V-REGION alignment according to the IMGT unique numbering", "3. V-REGION translation". The option "5. V-REGION protein display with colored AA according to the AA IMGT classes" is not more available.
- A. Detailed view, option "14. Annotation by IMGT/Automat": addition of the label D-J-REGION.
- "Results in Excel", "nt-sequences" sheet: addition of the label D-J-REGION.
- update of Mus musculus IGHV2-6-3*01 reference sequence.

15th of May 2009 (Version 3.2.3)
- Correction of a bug in the "V-REGION-nt-mutation-statistics" sheet of the Excel output.

5th of May 2009 (Version 3.2.2)
- Update of numbering for user sequences close to a reference sequence partial in 5'.

30th of April 2009 (Version 3.2.1)
- A. Detailed view results, "10. V-REGION mutation statistics": update of the presentation of the amino acid table

27th of April 2009 (Version 3.2.0)
- Addition of "Export in Excel file" output : the "Detailed view" results are recorded in 11 sheets.
- Query Page : the option "2. Alignment for D-GENE" of "A. Detailed view" is no more selected by default.
- A. Detailed view results:
  - In "Result summary", D-GENE(s) and allele(s) are shown only if identified by IMGT/JunctionAnalysis"
  - In "4. Results of IMGT/JunctionAnalysis"
    - In case of unmutated IGK or IGL V-GENE (no mutations in FR1-IMGT, CDR1-IMGT, FR2-IMGT, CDR2-IMGT and FR3-IMGT), the number of allowed mutations in 3'V-REGION and 5'J-REGION has been set to 2.
    - The number of accepted D-GENE in the junction is indicated
  - In "10. V-REGION mutation statistics": update of the presentation of the amino acid table
  - In "11. V-REGION mutation hot spots": the tables are displayed as follow: (a/t)a, t(a/t), (a/g)g(c/t)(a/t), (a/t)(a/g)c(c/t)
  - In "13. Sequences of V-, V-J- or V-D-J- REGION ('nt' and 'AA') with gaps in FASTA": the V-J- or V-D-J- REGION amino acid sequences are shown in red for unproductive sequences with an out-of-frame junction.
- "Export in text" output : elimination of HTML tags (except for option "5. V-REGION protein display with colored AA according to the AA IMGT classes" of Synthesis View).
- "B. Synthesis view results": in "7. V-REGION most frequently occurring AA per position and per FR-IMGT and CDR-IMGT", a message is added when, at a given position, 100% of the analyzed sequences have the same AA change.
- Update of IMGT gap positions in Homo sapiens IGHV3-72*02.
4th of February 2009 (Version 3.1.6)
- Addition of Rattus norvegicus IGHV2S58*01 and IGHV5S2*01

4th of December 2008 (Version 3.1.5)
- Addition of a new Rattus norvegicus IGLJ gene and allele: IGLJ4*01

19th of November 2008 (Version 3.1.4)
- Addition of Mus musculus TRAJ26*01 allele

23th of October 2008 (Version 3.1.3)
- Addition of a new Rattus norvegicus IGHD gene and allele: IGHD3-4*01
- The pseudogene Homo sapiens IGHV3-g*01 gene has been removed from the IMGT reference directory : it corresponds to the Homo sapiens mapped pseudogene IGHV3-71*01

18th of July 2008 (Version 3.1.2)
- Addition of 4 new Homo sapiens IGKV genes and alleles: IGKV1-16*02, IGKV1D-17*02, IGKV2-30*02 and IGKV3-7*04
- Correction of a bug in Detailed view "10. V-REGION mutation statistics" for the evaluation of amino acid number per IMGT label in case of amino acid changes at the end the 3'V-REGION

4th of July 2008 (Version 3.1.1)
- Addition of 7 Rattus norvegicus IGLV and 3 Rattus norvegicus IGLJ genes and alleles
- Improvement of Detailed view "10. V-REGION mutation statistics"
- Translation of the JUNCTION" when the option "Export in text" has been selected, has been slightly modified in order to be closer to the HTML format. In addition, Molecular mass and Pi of out-of-frame junctions are indicated as NR (not relevant).
- Correction of a small bug in the V numbering of partial sequences

18th of March 2008 (Version 3.1.0)
- Addition of an option in Selection for results display, Detailed view: "V-REGION protein display"

19th of February 2008 (Version 3.0.0)
- From this release, gaps in CDR1-IMGT and CDR2-IMGT are placed at the top of the loops

8th of February 2008 (Version 2.5.1)
- Addition of Homo sapiens IGHV3-49*04, IGHV3-49*05 and IGHV4-39*07 alleles

29th of January 2008 (Version 2.5.0)
- Addition of an option in Advanced parameters: "Search for insertions and deletions"
- Update of Rattus norvegicus IGHV reference directory
- Update of Mus musculus IGHV reference directory

12th of December 2007 (Version 2.4.5)
- Correction of a small bug in the detection of the closest Mus musculus genes and alleles.
- Update of the Mus musculus IGHV reference directory.

6th of December 2007 (Version 2.4.4)
- Update of Rattus norvegicus IGHV reference directory : subgroups IGHV1, IGHV2, IGHV3, IGHV4, IGHV5, IGHV6, IGHV7, IGHV8, IGHV9, IGHV10, IGHV11, IGHV12, IGHV13 and IGHV14 included
- Update of the Mus musculus IGHV reference directory.
8th of November 2007 (Version 2.4.3)
- In the Result sumary table, a note (a) appears with the functionality when the V identity percentage is less than 85% and/or when the closest germline and the analysed sequence show different CDR1-IMGT and/or CDR2-IMGT amino acid lengths in order to point out potential nucleotide insertion(s) and/or deletion(s).

14th of September 2007 (Version 2.4.2)
- Input sequence treatment: 5' and 3' terminal "n" nucleotides are automatically removed until the first 5' and 3' non "n" nucleotide, respectively
- Addition of Homo sapiens IGHV1-69*12, IGHV1-69*13, TRAJ13*02, TRGJ1*02, TRBV23/OR9-2*02 alleles
- Addition of Mus musculusIGKV17/OR19-2*01, IGKV17/OR16-3*01 and IGKV17/OR19-2*01 genes, and TRAJ21*02 allele
- The allele Mus musculus IGHV1-11*02 has been assigned to IGHV1-84*02.
- The allele Mus musculus IGHV3S4*01 has been assigned to IGHV3-3*03.
25th of July 2007 (Version 2.4.1)
- Addition of 10 Mus musculus IGHV genes:
  IGHV1-19-1*01, IGHV1-17-1*01, IGHV1-21-1*01, IGHV1-62-1*01, IGHV1-62-2*01,IGHV1-62-3*01, IGHV2-6*03, IGHV2-6-8*01, IGHV5-9-1*02, IGHV14-4*01
20th of July 2007 (Version 2.4.0)
- Addition of 17 Mus musculus IGHV genes:
  IGHV1-70*01, IGHV1-71*01, IGHV1-72*01, IGHV8-13*01, IGHV1-74*01, IGHV8-14*01, IGHV1-75*01, IGHV1-76*01, IGHV1-77*01, IGHV1-78*01, IGHV1-79*01, IGHV1-80*01, IGHV1-81*01, IGHV1-82*01, IGHV1-83*01, IGHV1-84*01, IGHV1-85*01
- Addition of a new species: rat (Rattus norvegicus)
  - 83 IGHV (test for IGHV2 and IGHV5 subgroups)
  - 19 IGHD
  - 4 IGHJ

6th of July 2007 (Version 2.3.0)
- A summary of the IMGT/V-QUEST results are provided in both Detailed view and Synthesis view.
- The "Advanced parameters" section has been added at the bottom of the IMGT/V-QUEST query page. It allows:
  - to select the IMGT/V-QUEST reference directory set.
  - to define if the user sequences will be compared with all alleles or with only the allele *01 of the genes of the IMGT/V-QUEST reference directory set.
  - to set the number of D-GENEs to be allowed in the IGH, TRB and TRD JUNCTIONs for IMGT/JunctionAnalysis.
  - to set the number of accepted mutations in 3'V-REGION, D-REGION and 5'J-REGION for IMGT/JunctionAnalysis.
  - to set the number of nucleotides to exclude in 5' of the V-REGION for V-REGION mutation table and V-REGION mutation statistics (for Detailed view results number 8 and 9).
  - to set the number of nucleotides to add or to exclude in 3' of the V-REGION for the evaluation of the alignment score (for Detailed view result 1).
- in-frame pseudogenes and orphons have been included in the IMGT/V-QUEST reference directory sets.

10th of April 2007 (Version 2.2.0)

The gene and allele functionality is only shown for pseudogene (P) and "ORF" (ORF) between parentheses.
In 4. Results of IMGT/JunctionAnalysis, JUNCTION amino acids are colored according to the IMGT amino acid classes for chemical characteristics [8].
In 4 .Results of IMGT/JunctionAnalysis, in case of frameshifts, they are indicated by a #.
Update of the human IMGT reference directory set: addition of in-frame pseudogenes (with at most one stop codon)
IGHV: IGHV1-68*01, IGHV3-22*01, IGHV3-22*02, IGHV3-25*03, IGHV3-52*01, IGHV3-52*02, IGHV3-52*03, IGHV3-71*01, IGHV5-78*01
IGKV: IGKV2-4*01, IGKV2-18*01, IGKV2D-18*01, IGKV7-3*01
IGLV: IGLV3-13*01

15th of November 2006 (Version 2.1.0)
IMGT/V-QUEST has been upgraded to provide a Synthesis view of results. The Synthesis view provides alignements of user sequences which express the same V allele, including
1. Alignment for V-GENE
2. V-REGION alignment
3. V-REGION translation
4. V-REGION protein Display
5. V-REGION protein Display with colored AA according to IMGT AA classes
6. V-REGION protein Display (mutations displayed)
7. V-REGION most frequently occurring AA per position and per FR-IMGT and CDR-IMGT
8. Results of IMGT/JunctionAnalysis

11th of May 2006 (Version 2.0.0)

IMGT/V-QUEST has been upgraded for multiple sequences and with new functionalities:
1. IMGT/V-QUEST is able to analyse sereral nucleotide sequences in a single run.
  Note that:
  - The sequences must be in FASTA format as shown in the "IMGT/V-QUEST selection and input" section.
  - More than 10 sequences submitted in a single run will cause potential slow answer.
  - The number of submitted sequences in a single run has been limited to 50.
2. New functionalities:
  - IMGT/V-QUEST is able to analyse inverse complementary sequences.
  - Nucleotide letters are always in lower cases, amino acids letters are always in upper cases.
  - The user may set the number of accepted D-GENE(s) in IGH, TRB and TRD JUNCTIONs for IMGT/JuntionAnalysis.
  - The user may visualize all eligible D-GENE(s) in IGH, TRB and TRD JUNCTIONs found by IMGT/JuntionAnalysis).
  - The IMGT Colliers de Perles include the representation of the CDR3-IMGT loop and are available:
    - in PNG (Portable Network Graphics) format
    - in interactive SGV (Scalable Vector Graphics) format (IMGT Collier de Perles on one layer and on two layers).
    SGV files require an SVG viewer (Firefox 1.5 or Internet explorer with Adobe SVG browser).
  - IMGT/V-QUEST performs additional analysis for the V-REGION as shown in IMGT/V-QUEST output:
    - V-REGION mutation table,
    - V-REGION mutation statistics,
    - V-REGION mutation hot spots.
  - IMGT/V-QUEST provides the automatic annotations of your input sequence(s) using IMGT/Automat [3]
  - The 3' end of the V-REGION is defined by IMGT/JunctionAnalysis. If not, it is set downstream of the last 2 nucleotides in 3' that are identical to the closest germline V-REGION.
  - IMGT/V-QUEST performs the numbering of the CDR3-IMGT according to the IMGT unique numbering.
  - The user may select the types of results he wants to display.
  - The user may select the number of nucleotides per line in the alignments (60, 90, 120, 150 or 10,000).
  - The user may set a number of nucleotides to exclude in 5' of the V-REGION, for instance when the primer used for the PCR amplification is located at the beginning of the FR1-IMGT. The excluded nucleotides will not be taken into account in V-REGION mutation table and in V-REGION mutation statistics

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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