IMGT/V-QUEST Documentation WELCOME !
IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org

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 program versions
IMGT/V-QUEST reference directory releases


Introduction

IMGT/V-QUEST (V-QUEry and STandardization) [1, 12] at Montpellier is an integrated alignment tool for the immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences. IMGT/V-QUEST compares your germline or rearranged IG or TR variable sequences with the IMGT/V-QUEST reference directory sets.

The IMGT/V-QUEST ouput displays are according to the IMGT Scientific chart rules and IMGT Repertoire.

Note that :

Sets of sequences to test IMGT/V-QUEST functionalities

IMGT/V-QUEST selection and input

IMGT/V-QUEST is available from the IMGT Home page for IG and TR rearranged sequences of different species.

The list of supported species and the IMGT/V-QUEST reference directory sets per locus to which your sequences can be compared is available here.

In the IMGT/V-QUEST Search page select the species and the antigen receptor (Immunoglobulin or T cell receptor) or locus.

The Search page includes five sections :

IMGT/V-QUEST reference directory sets

IMGT/V-QUEST output

A. Detailed view

Top of the IMGT/V-QUEST result page

The top of the IMGT/V-QUEST result page indicates:
- the IMGT/V-QUEST programme version,
- the IMGT/V-QUEST reference directory release

and recalls the parameters selected in the IMGT/V-QUEST Search page:
- Species: for example, Homo sapiens
- Receptor type or locus: IG or TR
- IMGT reference directory set: for example, F+ORF+in frame P (by default)
- Search for insertions and deletions: yes or no
- The "Nb of nucleotides to add (or exclude) in 3' of the V-REGION for the evaluation of the alignment score" and "Nb of nucleotides to exclude in 5' of the V-REGION for the evaluation of the nb of mutations" are indicated if default values have been modified in the Search page.

- The "Analysis of single chain Fragment variable (scFv)" is indicated if the option is selected

The number of analysed sequences is displayed with the list.
The name of each sequence is directly linked to its corresponding results.

For each analysed sequence, the IMGT reference directory set used for the alignments (for example, human IG set) is indicated.
The sequence is displayed in FASTA format.
The delimitation of the V-DOMAIN identified and analysed by IMGT/V-QUEST is highlighted in green.

If an input sequence was provided in the antisense orientation, IMGT/V-QUEST complementary reverses it automatically, and the results will be shown on the complementary reverse sequence (that is in "sense" orientation for the V-GENE) .

Result summary

A summary of the results is provided as a table. The Result summary table provides:

Note that the letters between parenthesis appear in the order that the warnings are detected.

Results

The results may include (if selected in the input page):

  1. Alignment for V-GENE and allele identification
  2. Alignment for D-GENE and allele identification
  3. Alignment for J-GENE and allele identification
  4. Results of IMGT/JunctionAnalysis
  5. Sequence of the JUNCTION ('nt' and 'AA')
  6. V-REGION alignment
  7. V-REGION translation
  8. V-REGION protein display
  9. V-REGION mutation and AA change table
  10. V-REGION mutation and AA change statistics
  11. V-REGION mutation hotspots
  12. Sequences of V-, V-J- or V-D-J- REGION ('nt' and 'AA') with gaps in FASTA.
  13. Annotations by IMGT/Automat
  14. IMGT Collier de Perles

Note that sequence names longer than 35 characters are truncated in the alignments and in the Results of IMGT/JunctionAnalysis.

Example : the sequence of AF184762 accession number.

  1. Alignment for V-GENE and allele identification


    This alignment shows your sequence aligned with the closest V-REGION alleles from the IMGT/V-QUEST reference directory sets. Dashes indicate identical nucleotides. Dots indicate gaps according to the IMGT unique numbering or nucleotides that are not taken into account for the alignments.

  2. Alignment for D-GENE and allele identification

    If this option has been selected in the query page, this alignment shows your sequence aligned with the closest D-REGION alleles from the IMGT/V-QUEST reference directory sets. Dashes indicate identical nucleotides. Dots indicate gaps according to the IMGT unique numbering or nucleotides that are not taken into account for the alignments.

  3. Alignment for J-GENE and allele identification.
    This alignment shows your sequence aligned with the closest J-REGION alleles from the IMGT/V-QUEST reference directory sets. Dashes indicate identical nucleotides. Dots indicate gaps according to the IMGT unique numbering or nucleotides that are not taken into account for the alignments.


  4. Results of IMGT/JunctionAnalysis.

    Depending on the selection you made in the IMGT/V-QUEST input page, and depending on your sequence, the results of IMGT/JunctionAnalysis [4] or the translation of the JUNCTION will be displayed.

    Note that IMGT/JunctionAnalysis gives no results when:

    If, in the current conditions, IMGT/JunctionAnalysis is unable to provide a result, the sequence of the JUNCTION is shown (see below). as well as the JUNCTION nucleotide sequence formatted for the IMGT/JunctionAnalysis tool.

  5. Sequence of the JUNCTION ('nt' and 'AA')

    The sequence of the JUNCTION is diplayed in nucleotide and in amino acid with the IMGT unique numbering.

    Sequence of the JUNCTION ('nt' and 'AA') displays the sequence of the JUNCTION and its translation, independently of its analysis by IMGT/JunctionAnalysis, as it is in the sequence analysed by IMGT/V-QUEST. If the option 'Search for insertions and deletions in V-REGION' has been selected, the deletions identified in the 3'V-REGION are shown as gaps and the insertions identified in the 3'V-REGION are deleted. The 3'V-REGION is translated accordingly and the translation is then continued in the 3' part without any other modification.

  6. V-REGION alignment according to the IMGT unique numbering

    The sequences are shown with the IMGT unique numbering and with the IMGT framework region ( FR-IMGT) and complementarity determining region ( CDR-IMGT) delimitations. Dashes indicate identical nucleotides. Dots indicate gaps according to the IMGT unique numbering.




    The resulting alignment shows the CDR3-IMGT of the germline V-REGION alleles of the IMGT reference directory sets. The CDR3-IMGT of the input rearranged sequence has to be identified in the translation of the JUNCTION (see above).
    The correct amino acid numbering of the rearranged CDR3-IMGT is the one shown in the Results of IMGT/JunctionAnalysis or translation of the JUNCTION

  7. V-REGION translation

    The "Translation of the input sequence" shows the nucleotide sequence and deduced amino acid translation of the input sequence, aligned with the V-REGION of the closest germline V-GENE, and with the FR-IMGT and CDR-IMGT delimitations.
    The 3' limit of the CDR3-IMGT of the input rearranged sequence is correctly identified if the conserved Phe/Trp-Gly-X-Gly motif of the J-REGION has been identified. If not, the 3' limit of the CDR3-IMGT needs to be checked
    The correct amino acid numbering of the rearranged CDR3-IMGT is the one shown in the Results of IMGT/JunctionAnalysis or translation of the JUNCTION




  8. V-REGION protein display.

    The "V-REGION protein display" shows the deduced amino acid translation of the input sequence, aligned with the V-REGION of the closest germline V-GENE, and with the FR-IMGT and CDR-IMGT delimitations.
    On the third line of the alignment are shown in bold, the input sequence amino acids which different from the closest germline.




  9. V-REGION mutation and AA change table

    The "V-REGION mutation and AA change table" shows the mutations of the input sequence by comparison with the V-REGION of the closest germline V-GENE. Mutations are described according to the IMGT Scientific chart rules and according to the IMGT unique numbering for V-REGION. Mutations are shown for FR1-IMGT, CDR1-IMGT, FR2-IMGT, CDR2-IMGT, FR3-IMGT and for the part of the CDR3-IMGT which can be compared with the V-REGION .

    IMGT mutation and AA change description

    IMGT mutations and AA changes are described as follows:

    Nonsilent mutation: mutation with AA change

    If the mutation is nonsilent, the nucleotide mutation is described, followed by a comma and the corresponding amino acid change: "t88>c, F30>L" means that the nucleotide "t" at position 88 of the V-REGION of the closest germline V-GENE has been mutated to "c" ("t88>c") and that the amino acid "F" at position 30 has been changed to "L" ("F30>L").
    For each amino acid change, the IMGT amino acid classes [8] that are conserved despite the amino acid change are indicated with "+" between parentheses in the following order: hydropathy, volume, chemical characteristics. For example, F30>L (+ - -) indicates that the two amino acids, F and L, belongs to the same hydropathy class but that the volume and the chemical characteristics classes are different.

    The AA changes are qualified as:

    • Very similar: (+ + +)
    • Similar: (+ + -) or (+ - +)
    • Dissimilar: (+ - -) or (- + -) or (- - +)
    • Very dissimilar: (- - -)

    As a consequence, two compared AA are qualified as:

    • Identical
    • Very similar
    • Similar
    • Dissimilar
    • Very dissimilar

    Silent mutation: mutation without AA change

    If the mutation is silent, the amino acid is identical in the V-REGION of the closest germline V-GENE and in the mutated sequence. Therefore the field on AA change (">" ) and IMGT amino acid classes changes are not shown: "g36>a, L12" means that the nucleotide "g" at position 36 of the V-REGION of the closest germline V-GENE has been mutated to "a" ("g36>a") and that the amino acid "L" at position 12 is unchanged in the mutated sequence ("L12").

    IMGT note: No amino acid is indicated if the mutated nucleotide is not in a codon (for example, "a320>g" at the end of the CDR3-IMGT)




  10. V-REGION mutation and AA change statistics

    The "V-REGION mutation and AA change statistics" shows the number of mutations and amino acid changes, by comparison with the V-REGION of the closest germline V-GENE. Numbers of mutations and amino acid changes are shown for the whole V-REGION, the FR1-IMGT, CDR1-IMGT, FR2-IMGT, CDR2-IMGT, FR3-IMGT and the part of the CDR3-IMGT which can be compared with the V-REGION.

    Note that the number of mutations for the V-REGION and the CDR3-IMGT are calculated with the 3' end delimitation determined by IMGT/JunctionAnalysis. Numbers added between parentheses for the V-REGION and the CDR3-IMGT indicate the number of nucleotide differences without taking into account the shortening of the V-REGION. These numbers include nucleotide differences that result from the N-diversity.

    Nucleotides : the number of silent and nonsilent mutations is evaluated, as well as each type of transition and transversion.
    Amino acids : The number of identical AA and AA changes is evaluated as well as each type of AA changes.



  11. V-REGION mutation hotspots

  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')

    The sequences of the V-, V-J- or V-D-J- REGION (in nucleotides ('nt') and in amino acids ('AA')) are displayed, in FASTA format, with gaps according to the IMGT unique numbering. Amino acid sequences are also displayed on one line.




    Note that the V-J- or V-D-J- REGION amino acid sequences are shown in red for unproductive sequences with an out-of-frame junction.

    Note that if the V-J- or V-D-J- REGION amino acid sequences are used in the IMGT/Collier-de-Perles tool online, the CDR3-IMGT length needs to be indicated in the appropriate window. For information, gaps of CDR3-IMGT shorter than 13 amino acids are not shown in the V-J- or V-D-J- REGION in FASTA format or on one line.

  13. Annotation by IMGT/Automat

    The annotation of the V-REGION, V-J-REGION and /or V-D-J-REGION of the input sequence is provided by IMGT/Automat [9].



  14. IMGT Collier de Perles for the input sequence V-DOMAIN

    The following information is provided: The CDR-IMGT and FR-IMGT lengths are based on the IMGT unique numbering for V-DOMAIN.

    By default, the link to the IMGT/Collier-de-Perles tool is provided.



    Clicking on the link provides access to the IMGT Collier de Perles generated by the IMGT/Collier-de-Perles tool program (originally developed by Gérard Mennessier (LPM, Montpellier, France), Manuel Ruiz, Quentin Kaas and François Ehrenmann (LIGM, Montpellier, France)),

    The IMGT IMGT/Collier de Perles for V-DOMAIN are according to the IMGT unique numbering for V-DOMAIN [7].
    IMGT amino acid classes (hydropathy, volume, chemical characteristics) are according to Pommié et al [8].




    Note that: If the option "IMGT Collier de Perles (for a nb of sequences < 5)" has been selected in "Display results" of the Search page, the Collier de Perles in PNG format is shown directly in the results page (except for TR alpha sequences because IMGT Collier de perles may be wrongly displayed for some submitted sequences).



Results for scFv

On the top of the result page, a table summarizes the identified scFv.
The table includes one line per scFv with the sequence identifier, the 5'V-DOMAIN ID, the 5'V-DOMAIN positions in the sequence, the 5'V-DOMAIN lengths, positions and length of the "linker" between the 2 V-DOMAIN, the 3'V-DOMAIN ID, the 3'V-DOMAIN positions in the sequence and the 3'V-DOMAIN lengths, respectively.

V Each V-DOMAIN is named with the sequence identifier followed by an "_" (underscore) and a capital letter for the locus (H, K, L for IGH, IGK and IGL, and A, B, D and G for TRA, TRB, TRD and TRG, respectively).

The link associated to the V-DOMAIN ID leads to the corresponding detailed results as described in IMGT/V-QUEST ouput.
On the top of the detailed results for each V-DOMAIN, the associated V-DOMAIN identifier is indicated between parentheses and the results of this domain can be reached by clicking on the link.

B. Synthesis view

Top of the IMGT/V-QUEST result page

The top of the IMGT/V-QUEST result page indicates:
- the IMGT/V-QUEST program version,
- the IMGT/V-QUEST reference directory release

and recalls the parameters selected in the IMGT/V-QUEST Search page:
- Species: for example, Homo sapiens
- Receptor type or locus: IG or TR
- IMGT reference directory set: for example, F+ORF+in frame P (by default)
- Search for insertions and deletions: yes or no
- The "Nb of nucleotides to add (or exclude) in 3' of the V-REGION for the evaluation of the alignment score" and "Nb of nucleotides to exclude in 5' of the V-REGION for the evaluation of the nb of mutations" are indicated if default values have been modified in the Search page.

- The "Analysis of single chain Fragment variable (scFv)" is indicated if the option is selected

The number of analysed sequences is displayed.

Summary Table

The result summary is provided as a table with one row for each input sequence, including:

Results of IMGT/JunctionAnalysis

Links to the results of IMGT/JunctionAnalysis for the junctions are provided .

Alignment with the closest alleles

The names of the closest V-GENE alleles with which your sequences have been aligned are shown, with the number of sequences aligned to each allele indicated between parentheses.
The name of each allele is directly linked to its corresponding results.

Results for each V-GENE and allele

The results may include (if selected in the input page):

  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

Note that sequence names longer than 35 characters are truncated in the alignments and in the Results of IMGT/JunctionAnalysis.

Example : the sequence of AF184762 accession number.



  1. Alignment for V-GENE


    This alignment shows your sequences which express the same V aligned with the closest V-REGION allele from the IMGT/V-QUEST reference directory sets. Dashes indicate identical nucleotides. Dots indicate gaps according to the IMGT unique numbering or nucleotides that are not taken into account for the alignments.

  2. V-REGION alignment.

    The sequences are shown with the IMGT unique numbering and with the IMGT framework region ( FR-IMGT) and complementarity determining region ( CDR-IMGT) delimitations. Dashes indicate identical nucleotides. Dots indicate gaps according to the IMGT unique numbering.




    The resulting alignment shows the CDR3-IMGT of the germline V-REGION alleles of the IMGT reference directory sets.

  3. V-REGION translation

    The "V-REGION Translation " shows the nucleotide sequence and deduced amino acid translation of the closest V-REGION aligned with the user sequences, and with the FR-IMGT and CDR-IMGT delimitations.




  4. V-REGION protein display

    The "V-REGION protein display" shows the V-REGION protein display of user sequences aligned with the closest V-REGION allele.




  5. V-REGION protein display (with AA class colors)

    The "V-REGION protein display" shows the V-REGION protein display of user sequences aligned with the closest V-REGION allele with colored AA according to the AA IMGT classes.




  6. V-REGION protein display (only AA changes displayed)

    The "V-REGION protein display" shows the V-REGION protein display of user sequences aligned with the closest V-REGION allele with only the mutations displayed.




  7. V-REGION most frequently occurring AA per position and per FR-IMGT and CDR-IMGT

    The "V-REGION most frequently occurring AA per position and per FR-IMGT and CDR-IMGT" shows a table, for each FR-IMGT and CDR-IMGT, indicating for each amino acid position the most frequently occurring AA.



  8. Results of IMGT/JunctionAnalysis

    The "Results of IMGT/JunctionAnalysis" shows the results of IMGT/JunctionAnalysis of JUNCTION user sequences per chain type, including Analysis of the JUNCTIONs and Translation of the JUNCTIONs

    Note that the "Results of IMGT/JunctionAnalysis" for Synthesis view is available for 'HTML' format only (not for 'Text' format).



Results for scFv

In the summary table, an scFv is identified by its number in the submitted files and by its sequence identifier.
The 2 V-DOMAIN of the scFv appears individually on consecutive lines of the table.

C. Excel file

For the option "Display 1 CSV file in your browser", the top of the IMGT/V-QUEST result page indicates:
- the IMGT/V-QUEST program version,
- the IMGT/V-QUEST reference directory release
and recalls the parameters selected in the IMGT/V-QUEST Search page:
- Species: for example, Homo sapiens
- Receptor type or locus: IG or TR
- IMGT reference directory set: for example, F+ORF+in frame P (by default)
- Search for insertions and deletions: yes or no
- The "Nb of nucleotides to add (or exclude) in 3' of the V-REGION for the evaluation of the alignment score" and "Nb of nucleotides to exclude in 5' of the V-REGION for the evaluation of the nb of mutations" are indicated if default values have been modified in the Search page.
- The "Analysis of single chain Fragment variable (scFv)" is indicated if the option is selected

The Excel file comprises 11 main sheets (equivalent for IMGT/HighV-QUEST to the 11 CSV files).

Note that a 12th file is added for Advanced functionalities, Analysis of single chain Fragment variable (scFv)

Table: Results content of the eleven (or twelve) IMGT/V-QUEST results spreadsheets or CSV files (and of IMGT/highV-QUEST CSV files) [13]. Citing this table [13].

Detailed columns are available by cliking on the "File name".


File number File name Number of columns filled Results content *
#1 "Summary" 30 (or 26) - Alignment score and identity percentage with the closest V and J genes and alleles,
- D-REGION reading frame,
- FR-IMGT and CDR-IMGT lengths,
- Amino acid (AA) JUNCTION,
- Description of insertions and deletions if any,
- User sequence in the direct orientation,
- Sequence orientation at the submission.
#2 "IMGT-gapped-nt-sequences" 18 - Nucleotide (nt) sequences gapped according to the IMGT unique numbering for the labels V-D-J-REGION, V-J-REGION, V-REGION, FR1-IMGT, CDR1-IMGT, FR2-IMGT, CDR2-IMGT, FR3-IMGT,
- nt sequences of CDR3-IMGT, JUNCTION, J-REGION and FR4-IMGT.
#3 "nt-sequences " 67, 81, 103 or 115 - nt sequences of all labels that can be automatically described and delimitated by IMGT/Automat (66 columns for IGL, IGK, TRA and TRG sequences, 81 (if one D), 102 (if two D) or 114 (if 3 D) columns for IGH, TRB and TRD sequences).
#4 "IMGT-gapped-AA-sequences" 18 - AA sequences gapped according to the IMGT unique numbering for the labels V-D-J-REGION, V-J-REGION, V-REGION, FR1-IMGT, CDR1-IMGT, FR2-IMGT, CDR2-IMGT, FR3-IMGT,
- AA sequences of CDR3-IMGT, JUNCTION, J-REGION and FR4-IMGT.
#5 "AA-sequences" 18 Same columns as "IMGT-gapped-AA-sequences" (#4), but sequences of labels are without IMGT gaps.
#6 "Junction" 40, 53, 73, or 84 - Results of IMGT/JunctionAnalysis (40 columns for IGL, IGK, TRA and TRG sequences, 53 (if one D), 73 (if two D) or 84 (if 3 D) columns for IGH, TRB and TRD sequences).
#7 "V-REGION-mutation-and-AA-change-table" 11 - List of mutations (nt mutations, AA changes, codon change, hotspot motifs, AA class identity (+) or change (-)) for V-REGION, FR1-IMGT, CDR1-IMGT, FR2-IMGT, CDR2-IMGT, FR3-IMGT and germline CDR3-IMGT.
#8 "V-REGION-nt-mutation-statistics " 130 - Number (nb) of nt positions including IMGT gaps, nb of nt, nb of identical nt, total nb of mutations, nb of silent mutations, nb of nonsilent mutations, nb of transitions (a>g, g>a, c>t, t>c) and nb of transversions (a>c, c>a, a>t, t>a, g>c, c>g, g>t, t>g) for V-REGION, FR1-IMGT, CDR1-IMGT, FR2-IMGT, CDR2-IMGT, FR3-IMGT and germline CDR3-IMGT.
#9 "V-REGION-AA-change-statistics " 109 - nb of AA positions including IMGT gaps, nb of AA, nb of identical AA, total nb of AA changes, nb of AA changes according to AAclassChangeType (+++, ++-, +-+, +--, -+-, --+, ---), and nb of AA class changes according to AAclassSimilarityDegree (nb of Very similar, nb of Similar, nb of Dissimilar, nb of Very dissimilar) for V-REGION, FR1-IMGT, CDR1-IMGT, FR2-IMGT, CDR2-IMGT, FR3-IMGT and germline CDR3-IMGT.
#10 " V-REGION-mutation-hotspots " 8 - Hot spots motifs ((a/t)a, t(a/t), (a/g)g(c/t)(a/t), (a/t)(a/g)c(c/t)) detected in the closest germline V-REGION with positions in FR-IMGT and CDR-IMGT.
#11 "Parameters " - Date of the analysis,
- IMGT/V-QUEST programme version, IMGT/V-QUEST reference directory release,
- Parameters used for the analysis: species, receptor type or locus, IMGT reference directory set and Advanced parameters.
#12 "scFv " 40 Available only for Advanced functionalities, Analysis of single chain Fragment variable (scFv).
- positions and length, CDR_length, JUNCTION for the 2 V-DOMAIN of the scFv
- positions and length of the linker
*: Files #1 to #10 and #12 comprise systematically sequence identification, i.e. the sequence name, the functionality, the names of the closest V gene and allele, and files #1 to #6 and #12 also include the D and J genes and alleles. The files #7 to #10 that report the analysis of mutations are used mostly for immunoglobulins (IG). Files #1 to #10 include one line per submitted sequence or V-DOMAIN. Files #12 includes one line per scFv

Detailed columns per spreadsheet or CSV file :

  1. The "Summary" spreadsheet includes:
  2. The "IMGT-gapped-nt-sequences" spreadsheet includes:

  3. The "nt-sequences" spreadsheet includes:

  4. The "IMGT-gapped-AA-sequences" spreadsheet includes:

  5. The "AA-sequences" spreadsheet includes:

  6. The "Junction" spreadsheet includes:

  7. The "V-REGION-mutation-table" spreadsheet includes:

    In a given field, mutations are separated with "|".
    The details for the description of a mutation are available in Correlation between V-REGION mutations, AA changes, codons changes and hotspots motifs)

  8. The "V-REGION-nt-mutation-statistics" spreadsheet includes:

  9. The "V-REGION-AA-mutation-statistics" spreadsheet includes:

  10. The "V-REGION-mutation-hotspots" spreadsheet includes:

  11. The "Parameters" spreadsheet includes the date of the analysis, and the general and advanced parameters used by IMGT/V-QUEST:
  12. The "scFv" sheet is available only for Advanced functionalities, Analysis of single chain Fragment variable (scFv).
    It includes 1 line per submitted sequence identified as an scFv (at least 2 V-REGION in the same sequence).
    One line comprises 2 groups of columns: one prefixed by "1_" for one V-DOMAIN and the second group prefixed by "2_" for the other V-DOMAIN of the scFv. They are separated by 2 columns for positions and length of the scFv linker sequence.

    In order to facilitate data extraction or reuse, fields corresponding to the IGH for IG, or to the TRB or TRD for TR V-DOMAIN are arbitrary in the "1_" column group, whatever their order (5' V-DOMAIN or 3' V-DOMAIN) in the submitted scFv sequence.

    Note that : Sequences not identified as scFv (with a single V-DOMAIN or a single V-REGION) are not integrated in this file, so the 12_ scFv spreadsheet or file can be empty if none of the submitted sequences are scFv.

D. Results provided following "Search for insertions and deletions" (Advanced parameters)

The option "Search for insertions and/or deletions" of Advanced parameters has to be selected at the bottom of the IMGT/V-QUEST Search page.

Note that:

Results provided in case of insertions

  1. in "Detailed view"

  2. in "Synthesis view"

  3. in "Excel file"

    Four additional columns are added in the Summary sheet:

    - V-REGION identity % (with ins/del events): it indicates 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.
    - V-REGION identity nt (with ins/del events): it indicates 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.
    - V-REGION insertions: it indicates the sequence, the length and the localization of the insertion(s).
    - V-REGION deletions: it indicates the localization and the length of the deletion(s).

    Note that : insertions appear in capital letters in the user sequence. The results provided in the other sheets of the Excel file correspond to the IMGT/V-QUEST analysis after removal of the insertions.

Results provided in case of deletions

  1. in "Detailed view"

  2. in "Synthesis view"

  3. in "Excel file"

    Three additional columns are added in the Summary sheet:

    - V-REGION identity % (with ins/del events): it indicates 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.
    - V-REGION identity nt (with ins/del events): it indicates 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.
    - V-REGION deletions: it indicates the localization of the deletion(s).

IMGT/V-QUEST annexes


References:
[1] Giudicelli, V. et al. Nucl. Acids Res. 32, W435-440 (2004) PMID: 15215425 LIGM:287
[2] Belessi C.J. et al. Eur J Immunol. 36, 1963-74 (2006). PMID: 16783849
[3] Giudicelli, V. et al. Stud. Health Technol. Inform. 116, 3-8 (2005) PMID:16160227 LIGM: 298
[4] Yousfi Monod, M. et al. Bioinformatics , 20, i379-i385 (2004) PMID: 15262823 LIGM:289
[5] Lefranc, M.-P. Methods Mol. Biol. 248, 27-49 (2004) PMID: 14970490 LIGM:277
[6] Lefranc, M.-P. Current Protocols in Immunology pp. A1W.1-A.1W.15 (2006) PMID: 18432961 LIGM:311
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