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

Joseph M. Volpe, Lindsay G. Cowell, Thomas B. Kepler

Research output: Contribution to journalArticle

92 Citations (Scopus)

Abstract

Motivation: The antigen receptors of adaptive immunity - T-cell receptors and immunoglobulins - are encoded by genes assembled stochastically from combinatorial libraries of gene segments. Immunoglobulin genes then experience further diversification through hypermutation. Analysis of the somatic genetics of the immune response depends explicitly on inference of the details of the recombinatorial process giving rise to each of the participating antigen receptor genes. We have developed a dynamic programming algorithm to perform this reconstruction and have implemented it as web-accessible software called SoDA (Somatic Diversification Analysis). Results: We tested SoDA against a set of 120 artificial immunoglobulin sequences generated by simulation of recombination and compared the results with two other widely used programs. SoDA inferred the correct gene segments more frequently than the other two programs. We further tested these programs using 30 human immunoglobulin genes from Genbank and here highlight instances where the recombinations inferred by the three programs differ. SoDA appears generally to find more likely recombinations.

Original languageEnglish (US)
Pages (from-to)438-444
Number of pages7
JournalBioinformatics
Volume22
Issue number4
DOIs
StatePublished - Feb 15 2006

Fingerprint

Immunoglobulin Genes
Antigen Receptors
Diversification
Antigens
Recombination
Receptor
Genetic Recombination
Immunoglobulin
Alignment
Genes
Immunoglobulins
Gene
Nucleic Acid Databases
Adaptive Immunity
T-Cell Antigen Receptor
Gene Library
Software
Dynamic programming
T-cells
Immune Response

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

SoDA : Implementation of a 3D alignment algorithm for inference of antigen receptor recombinations. / Volpe, Joseph M.; Cowell, Lindsay G.; Kepler, Thomas B.

In: Bioinformatics, Vol. 22, No. 4, 15.02.2006, p. 438-444.

Research output: Contribution to journalArticle

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