SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations
SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations
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DOI：
10.1093/bioinformatics/btk004
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发表时间：
2006-02-15
期刊：
影响因子：
5.8
通讯作者：
Kepler, TB
中科院分区：
文献类型：
--
作者：
Volpe, JM;Cowell, LG;Kepler, TB
动机：适应性免疫的抗原受体-T细胞受体和免疫球蛋白-由从基因片段组合文库随机组装的基因编码。免疫球蛋白基因然后经历通过超突变进一步多样化。免疫应答的体细胞遗传学分析明确地依赖于对引起每个参与抗原受体基因的重组过程的细节的推断。我们已经开发了一个动态规划算法来执行此重建，并已实现它作为Web访问的软件称为SoDA（体细胞多样化分析）。结果：我们测试了SoDA对一组120人工免疫球蛋白序列模拟重组产生的，并与其他两个广泛使用的程序的结果进行比较。SoDA比其他两个程序更频繁地推断出正确的基因片段。我们使用Genbank中的30个人免疫球蛋白基因进一步测试了这些程序，并在这里突出显示了三个程序推断的重组不同的情况。SoDA似乎通常发现更可能的重组。
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.