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VDJsolver 1.0 Server

The VDJsolver 1.0 server is a program that analyses human immunoglobulin VDJ recombination. The indetification of V and J genes is performed using standard sequencial alignment against databases of functional VH and JH genes from the IMGT database.

Sequences are aligned to the following model:

VH-PVH-N1-PDup-D-PDdown-N2-PJH-JH,

where Pxx designates palindromic nucleotide segments, and Nx N nucleotides upstream or downstream of D. The optimal alignment is obtained using maximum likelihood to select the best fit of the sequence to the model. In the fitting all segments except VH and JH may be omitted. The model includes all conventional germline D segments in the IMGT database (D gene list) in normal and inverted reading direction. For details on the model please see Model description

The project is collaboration between CBS and Clinical immunology, University of Southern Denmark.

       

Instructions Model description Output format Article abstract

SUBMISSION

Paste a single sequence or several sequences in FASTA format into the field below:

Submit a file in FASTA format directly from your local disk:

     

Save input in summary file 

Save output in summary file 

Restrictions:
At most 500 sequences per submission; each sequence not more than 10,000 basepairs.

Confidentiality:
The sequences are kept confidential and will be deleted after processing.


CITATIONS

For publication of results, please cite:

  • Current version:
    No evidence for the use of DIR, D-D fusions, chromosome 15 open reading frames or VH replacement in the peripheral repertoire was found on application of an improved algorithm, JointML, to 6329 human immunoglobulin H rearrangements.
    Ohm-Laursen L, Nielsen M, Larsen SR, and Barington T.
    Immunology. 119(2):265-77. 2006

    View the abstract        


PORTABLE VERSION

Would you prefer to run VDJsolver at your own site? VDJsolver v. 1.0 is available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms. There is a download page for academic users; other users are requested to contact CBS Software Package Manager at software@cbs.dtu.dk.


GETTING HELP

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