SoDA specifications

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This program is currently not supported, it has been replaced by Cloanalyst.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

SoDA in publications

 (3)
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 […]

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) […]

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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