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

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

doi:10.1093/bioinformatics/btk004

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 journal › Article › peer-review

103 Scopus citations

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 language	English (US)
Pages (from-to)	438-444
Number of pages	7
Journal	Bioinformatics
Volume	22
Issue number	4
DOIs	https://doi.org/10.1093/bioinformatics/btk004
State	Published - Feb 15 2006

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

Access to Document

10.1093/bioinformatics/btk004

Cite this

@article{df9c9e3b63a345d6a790f94efd1edb4d,

title = "SoDA: Implementation of a 3D alignment algorithm for inference of antigen receptor recombinations",

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.",

author = "Volpe, {Joseph M.} and Cowell, {Lindsay G.} and Kepler, {Thomas B.}",

note = "Funding Information: J.M.V. would like to thank his colleagues in the Duke University Laboratory of Computational Immunology for helpful discussions during the genesis of this project and Duke University Graduate School for financial support. This research was made possible through the generous financial support of the Burroughs Wellcome Fund (Career Award 1004005 to L.G.C.) and of the National Institutes of Health (T.B.K.) through the Southeast Regional Center for Excellence in Emerging Infections and Biodefense (U54 AI057157-02; B Haynes) and the Duke Center for Translational Research (5P30 AI051445-01; B Haynes).",

year = "2006",

month = feb,

day = "15",

doi = "10.1093/bioinformatics/btk004",

language = "English (US)",

volume = "22",

pages = "438--444",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "4",

}

TY - JOUR

T1 - SoDA

T2 - Implementation of a 3D alignment algorithm for inference of antigen receptor recombinations

AU - Volpe, Joseph M.

AU - Cowell, Lindsay G.

AU - Kepler, Thomas B.

N1 - Funding Information: J.M.V. would like to thank his colleagues in the Duke University Laboratory of Computational Immunology for helpful discussions during the genesis of this project and Duke University Graduate School for financial support. This research was made possible through the generous financial support of the Burroughs Wellcome Fund (Career Award 1004005 to L.G.C.) and of the National Institutes of Health (T.B.K.) through the Southeast Regional Center for Excellence in Emerging Infections and Biodefense (U54 AI057157-02; B Haynes) and the Duke Center for Translational Research (5P30 AI051445-01; B Haynes).

PY - 2006/2/15

Y1 - 2006/2/15

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=32544437698&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=32544437698&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btk004

DO - 10.1093/bioinformatics/btk004

M3 - Article

C2 - 16357034

AN - SCOPUS:32544437698

SN - 1367-4803

VL - 22

SP - 438

EP - 444

JO - Bioinformatics

JF - Bioinformatics

IS - 4

ER -

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

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this