IMGT/JunctionAnalysis programme versions

IMGT/JunctionAnalysis programme versions

http://www.imgt.org

Citing IMGT/JunctionAnalysis:
Yousfi Monod, M. et al., Bioinformatics, 20, i379-i385 (2004). PMID: 15262823.

Giudicelli, V., Lefranc, M.-P., Cold Spring Harb Protoc. 2011 Jun 1;2011(6). pii: pdb.prot5634. doi: 10.1101/pdb.prot5634.
PMID: 21632777 Abstract also in IMGT booklet with generous provision from Cold Spring Harbor (CSH) Protocols

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IMGT/JunctionAnalysis programme version: 2.1.0 (29 November 2011) - IMGT/JunctionAnalysis reference directory release: 201211-1 (12 March 2012)

Version 2.1.0 (29th of November 2011)
- The format of the junctions is checked at the launching of the analysis: if errors are detected, they are listed and displayed altogether in the same "Message" page.
- Junctions with same identifier are allowed.
- In the result page: addition of the number of submitted junctions, the number of results and the number of junctions with no results.
- The list of junctions with no results is available at the bottom of the result page.
Version 2.0.3 (8th of November 2011)
- Improvement of the analysis of the junction for TRAV/DV-TRDJ and TRAV/DV-TRAJ sequences.
Version 2.0.2 (27th of June 2011)
- Update of the display of the IMGT gene and allele names: in the results, the 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).
- Display of a warning when 2 junctions have the same identifier.
Version 2.0.1 (29th of March 2011)
- Update of the display of IMGT/JunctionAnalysis search page.
Version 2.0.0 (17th of September 2010)
- The "Advanced parameters" section is directly available at the bottom of the IMGT/JunctionAnalysis Welcome page. It allows:
  - To modify the parameters for the analysis, if required:
    - "5' and 3' ends of the JUNCTION": "Default" means that the junction nucleotide sequences must start in 5' with a cystein ("tgt" or "tgc") codon and must end in 3' with a tryptophan ("tgg") or phenylalanine ("ttt" or "ttc") codon. Another alternative is that the junction "May start and/or end with any codon".
    - "Number of D-GENEs for IGH, TRB and TRD JUNCTION". Default values are 1 for IGH, 1 for TRB and 3 for TRD. You may modify it from 0 to 3.
    - "Number of accepted mutations": this option allows to modify the number of mutations that are accepted in the 3'V-REGION, D-REGION(s), and 5'J-REGION (see step 5 for default values). You may modify it from 0 to 10.
    - "Delimitation of 3'V-REGION, D-REGION and 5'J-REGION": "Default" is "using patterns" (see step 5). The other alternative is to "Stop trimming with the first encountered identical nucleotide".
    - "D-GENE choice (if several have the same score)": Default is "The less mutated one" (see step 5). The other alternatives are "The longest one" or the "The one more upstream in the locus".
  - To Modify the parameters for the display, if required:
    - "List of all eligible D-GENE": This option allows to visualize all D genes that match the junction and to compare their score. It is displayed by default when only one junction is analysed in the run.
    - "Colored IMGT AA classes and histogram": the coloration according to the IMGT AA classes is provided by default but can be eliminated.
    - Output order: the results in "JUNCTION alignments with translation and IMGT AA classes" may be displayed in "Same order as input" (default), "CDR3-IMGT length decreasing order" or "CDR3-IMGT length increasing order".

Created: 17/09/2010
Last updated: 7/03/2011

Use of this software should be cited as beeing part of "IMGT, the international ImMunoGeneTics information system® http://www.imgt.org (Initiator and coordinator: Marie-Paule Lefranc, Montpellier, France)" with the references: Lefranc, M.-P. et al., Nucleic Acids Res., 33, D593-D597 (2005) Full text, Lefranc, M.-P. et al., In Silico Biol., 5, 0006 (2005); 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.

IMGT initiator and coordinator: Marie-Paule Lefranc (Marie-Paule.Lefranc@igh.cnrs.fr)
Bioinformatics manager: Véronique Giudicelli (Veronique.Giudicelli@igh.cnrs.fr)
Computer manager: Patrice Duroux (Patrice.Duroux@igh.cnrs.fr)
Interface design: Chantal Ginestoux (Chantal.Ginestoux@igh.cnrs.fr)

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