IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.
IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.
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DOI：
10.1093/bioinformatics/btv238
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发表时间：
2015-06-15
期刊：
影响因子：
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通讯作者：
Pevzner PA
中科院分区：
文献类型：
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作者：
Safonova Y;Bonissone S;Kurpilyansky E;Starostina E;Lapidus A;Stinson J;DePalatis L;Sandoval W;Lill J;Pevzner PA
血清中循环抗体（抗体库）浓度的分析是免疫信息学中的一个基本问题，但研究甚少。目前分析抗体库的两种方法[下一代测序（NGS）和质谱（MS）]存在困难的计算挑战，因为抗体不是直接在种系中编码，而是通过体细胞重组和超突变而广泛多样化。因此，解释循环抗体光谱所需的蛋白质数据库是针对每个个体定制的。虽然这样的数据库可以通过NGS构建，但由NGS生成的读段是易错的，甚至单个核苷酸错误也会妨碍通过标准蛋白质组学工具鉴定肽。在这里，我们提出了IgRepertoireConstructor算法，该算法对免疫测序读数进行纠错，并使用质谱来验证构建的抗体库。可用性和实施：IgRepertoireConstructor是开源的，可以作为C++和Python程序在所有Unix兼容平台上免费使用。源代码可从http://bioinf.spbau.ru/igtools获得。联系方式：ppevzner@ucsd.edu补充信息：补充数据可从生物信息学在线网站获得。
The analysis of concentrations of circulating antibodies in serum (antibody repertoire) is a fundamental, yet poorly studied, problem in immunoinformatics. The two current approaches to the analysis of antibody repertoires [next generation sequencing (NGS) and mass spectrometry (MS)] present difficult computational challenges since antibodies are not directly encoded in the germline but are extensively diversified by somatic recombination and hypermutations. Therefore, the protein database required for the interpretation of spectra from circulating antibodies is custom for each individual. Although such a database can be constructed via NGS, the reads generated by NGS are error-prone and even a single nucleotide error precludes identification of a peptide by the standard proteomics tools. Here, we present the IgRepertoireConstructor algorithm that performs error-correction of immunosequencing reads and uses mass spectra to validate the constructed antibody repertoires. Availability and implementation: IgRepertoireConstructor is open source and freely available as a C++ and Python program running on all Unix-compatible platforms. The source code is available from http://bioinf.spbau.ru/igtools. Contact: ppevzner@ucsd.edu Supplementary information: Supplementary data are available at Bioinformatics online.