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V(D)J assignment Immunoglobulin rearrangement detection

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SoDA specifications

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Information

Unique identifier	OMICS_13775
Name	SoDA
Alternative name	Somatic Diversification Analysis
Interface	Web user interface
Restrictions to use	None
Computer skills	Basic
Stability	No
Maintained	No

Maintainer

This tool is not available anymore.

Additional information

This program is currently not supported, it has been replaced by Cloanalyst.

Publications for Somatic Diversification Analysis

SoDA2: a Hidden Markov Model approach for identification of immunoglobulin rearrangements.

2010 Bioinformatics

PMCID: 2844993

PMID: 20147303

DOI: 10.1093/bioinformatics/btq056

SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations.

2006 Bioinformatics

PMID: 16357034

SoDA in publications

(3)

Assigning and visualizing germline genes in antibody repertoires

PMCID: 4528417

PMID: 26194754

DOI: 10.1098/rstb.2014.0240

[…] clonally derived sequences., we compared igscueal with several other tools, including imgt/highv-quest v. 1.3.1 [], igblast v. 1.4.0 [] and ihmmune-align (1-06-2007) []. a binary version of soda (somatic diversification analysis, v. 1.1) was extracted from automation [], and python scripts were used to run soda for each query sequence and to parse the output. we also used vdjalign […]

Restricted isotype, distinct variable gene usage, and high rate of gp120 specificity of HIV 1 Envelope specific B cells in colostrum compared to those in blood of HIV 1 infected, lactating African women

PMCID: 4320043

PMID: 25100291

DOI: 10.1038/mi.2014.69

[…] the pcr products were purified and sequenced. ig isotype was determined by sequence homology, and somatic hypermutation frequencies, inferred v(d)j rearrangement, and cdr3 length were determined by somatic diversification analysis (soda), a web-based programming algorithm. overlapping pcr was performed to co-express the variable region pcr products with full length igg1 (for heavy chain) […]

Initial antibodies binding to HIV 1 gp41 in acutely infected subjects are polyreactive and highly mutated

PMCID: 3201211

PMID: 21987658

DOI: 10.1084/jem.20110363

[…] the trigger for further antibody affinity maturation., to directly test the hypothesis that autologous env reactivity in ahi clonal lineages can arise distal to a founder naive b cell, we used somatic diversification analysis-2 (soda-2; ; ) and dna maximum likelihood (, , ) programs to infer reverted unmutated ancestors (ruas) of clonal lineages 558, 572, 712, and 728 (; and tables s7–11) […]

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SoDA institution(s)

Center for Computational Immunology, Duke University, NC, USA; Computational Biology and Bioinformatics Program, Duke University, NC, USA; Department of Biostatistics and Bioinformatics, Durham, NC, USA

SoDA funding source(s)

This work was supported by the Bill and Melinda Gates Foundation through grant number 38643.

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