Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies.
Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies.
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Ab-origin：一种增强工具，用于识别重排抗体种系中的来源基因片段
DOI：
10.1186/1471-2105-9-s12-s20
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发表时间：
2008-12-12
影响因子：
3
通讯作者：
Cao Z
中科院分区：
文献类型：
--
作者：
Wang X;Wu D;Zheng S;Sun J;Tao L;Li Y;Cao Z
背景在适应性免疫系统中，免疫球蛋白的可变区（IG）是由可变（V）、多样性（D）和连接（J）基因片段在生殖细胞中随机重组而编码的。将功能性抗体序列分配到它们的来源种系基因区段不仅对于理解抗体成熟而且对于促进治疗性抗体的潜在工程化是至关重要的。迄今为止，已经开发了几种工具来执行这种“追溯”计算。然而，对于不同的数据集，这些工具的预测能力和处理量差异很大。此外，它们都没有给出免疫球蛋白重多样性（IGHD）鉴定的置信度。随着免疫学数据库的不断发展，迫切需要开发快速、高效、功能强大的免疫学数据库分析工具。它是基于经验知识、优化的评分方案和适当的参数，通过对生殖系数据库的批量查询而设计的。已作出特别努力，以提高短期和动荡的地区，IGHD的识别精度。特别是，一定的灵敏度和特异性的阈值得分提供给IGHD identification.ConclusionWhen使用不同的模拟数据和实验数据集进行评估的置信水平，AB-起源优于所有其他五个流行的工具在预测精度方面。IGHD标识的批量查询和置信度指示功能将为用户提供额外的帮助。该计划是免费提供的， http://mpsq.biosino.org/ab-origin/supplementary.html .
BackgroundIn the adaptive immune system, variable regions of immunoglobulin (IG) are encoded by random recombination of variable (V), diversity (D), and joining (J) gene segments in the germline. Partitioning the functional antibody sequences to their sourcing germline gene segments is vital not only for understanding antibody maturation but also for promoting the potential engineering of the therapeutic antibodies. To date, several tools have been developed to perform such "trace-back" calculations. Yet, the predicting ability and processing volume of those tools vary significantly for different sets of data. Moreover, none of them give a confidence for immunoglobulin heavy diversity (IGHD) identification. Developing fast, efficient and enhanced tools is always needed with the booming of immunological data.ResultsHere, a program named Ab-origin is presented. It is designed by batch query against germline databases based on empirical knowledge, optimized scoring scheme and appropriate parameters. Special efforts have been paid to improve the identification accuracy of the short and volatile region, IGHD. In particular, a threshold score for certain sensitivity and specificity is provided to give the confidence level of the IGHD identification.ConclusionWhen evaluated using different sets of both simulated data and experimental data, Ab-origin outperformed all the other five popular tools in terms of prediction accuracy. The features of batch query and confidence indication of IGHD identification would provide extra help to users. The program is freely available at http://mpsq.biosino.org/ab-origin/supplementary.html .