...
  • 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>BMC Bioinformatics >VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements
【24h】

VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements

机译：VDJML：一种文件格式，带有用于捕获推断免疫受体重排结果的工具

获取原文
           
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

Background The genes that produce antibodies and the immune receptors expressed on lymphocytes are not germline encoded; rather, they are somatically generated in each developing lymphocyte by a process called V(D)J recombination, which assembles specific, independent gene segments into mature composite genes. The full set of composite genes in an individual at a single point in time is referred to as the immune repertoire. V(D)J recombination is the distinguishing feature of adaptive immunity and enables effective immune responses against an essentially infinite array of antigens. Characterization of immune repertoires is critical in both basic research and clinical contexts. Recent technological advances in repertoire profiling via high-throughput sequencing have resulted in an explosion of research activity in the field. This has been accompanied by a proliferation of software tools for analysis of repertoire sequencing data. Despite the widespread use of immune repertoire profiling and analysis software, there is currently no standardized format for output files from V(D)J analysis. Researchers utilize software such as IgBLAST and IMGT/High V-QUEST to perform V(D)J analysis and infer the structure of germline rearrangements. However, each of these software tools produces results in a different file format, and can annotate the same result using different labels. These differences make it challenging for users to perform additional downstream analyses. Results To help address this problem, we propose a standardized file format for representing V(D)J analysis results. The proposed format, VDJML, provides a common standardized format for different V(D)J analysis applications to facilitate downstream processing of the results in an application-agnostic manner. The VDJML file format specification is accompanied by a support library, written in C++ and Python, for reading and writing the VDJML file format. Conclusions The VDJML suite will allow users to streamline their V(D)J analysis and facilitate the sharing of scientific knowledge within the community. The VDJML suite and documentation are available from https://vdjserver.org/vdjml/ . We welcome participation from the community in developing the file format standard, as well as code contributions.
机译：背景技术产生抗体的基因和在淋巴细胞上表达的免疫受体不是由种系编码的，而是由种系编码的。相反，它们是通过称为V（D）J重组的过程在每个发育中的淋巴细胞中体细胞生成的，该过程将特定的独立基因片段组装成成熟的复合基因。个体在单个时间点的完整复合基因集合称为免疫库。 V（D）J重组是适应性免疫的显着特征，可针对基本上无限的抗原阵列实现有效的免疫反应。免疫库的表征在基础研究和临床环境中都是至关重要的。通过高通量测序在库谱分析方面的最新技术进步已导致该领域的研究活动激增。随之而来的是用于库全序列数据分析的软件工具的激增。尽管广泛使用了免疫库分析和分析软件，但目前尚无用于V（D）J分析的输出文件的标准化格式。研究人员利用IgBLAST和IMGT / High V-QUEST等软件进行V（D）J分析并推断种系重排的结构。但是，这些软件工具中的每一个都会以不同的文件格式生成结果，并且可以使用不同的标签来注释相同的结果。这些差异使用户难以进行其他下游分析。结果为了帮助解决此问题，我们提出了一种标准的文件格式来表示V（D）J分析结果。提议的格式VDJML为不同的V（D）J分析应用程序提供了一种通用的标准化格式，从而以与应用程序无关的方式促进了结果的下游处理。 VDJML文件格式规范随附有一个支持库，该支持库用C ++和Python编写，用于读取和写入VDJML文件格式。结论VDJML套件将允许用户简化他们的V（D）J分析，并促进社区内科学知识的共享。可从https://vdjserver.org/vdjml/获得VDJML套件和文档。我们欢迎社区参与开发文件格式标准以及代码贡献。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号