IgMAT: immunoglobulin sequence multi-species annotation tool for any species including those with incomplete antibody annotation or unusual characteristics.
IgMAT: immunoglobulin sequence multi-species annotation tool for any species including those with incomplete antibody annotation or unusual characteristics.
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DOI：
10.1186/s12859-023-05624-2
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发表时间：
2023-12-21
影响因子：
3
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中科院分区：
文献类型：
--
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高通量测序技术的出现和不断改进，使得免疫球蛋白库测序无论研究物种如何都可以获得和提供信息。然而，为了全面了解多克隆反应的动态变化，精确的框架和互补性决定重排基因的区域注释是关键。大多数序列注释工具主要是为人类和小鼠抗体序列设计的，这些序列使用具有固定物种列表的数据库，应用非常具体的假设来选择独特的结构特征。出于这个原因，能够从呈现的数据中学习的数据不可知工具对于新物种或新数据集非常有用。我们已经开发了IgMAT，它利用了一个减少的氨基酸字母表，将多个HMM对齐合并到一个单一的共识中，以自动注释来自大多数生物体的免疫球蛋白序列。此外，该软件允许合并用户定义的数据库，以更好地表示感兴趣的物种和/或抗体类别。为了证明IgMAT的准确性和实用性，我们分析了从几个不同物种的结构数据和免疫球蛋白序列数据集中提取的序列。IgMAT是完全开源的，可以在GitHub （https://github.com/TPI-Immunogenetics/igmat）上免费下载，遵循GPLv3许可。它可以用作CLI应用程序，也可以用作集成在自定义脚本中的python模块。在线版本包含补充材料，可在10.1186/s12859-023-05624-2获得。
The advent and continual improvement of high-throughput sequencing technologies has made immunoglobulin repertoire sequencing accessible and informative regardless of study species. However, to fully map dynamic changes in polyclonal responses precise framework and complementarity determining region annotation of rearranging genes is pivotal. Most sequence annotation tools are designed primarily for use with human and mouse antibody sequences which use databases with fixed species lists, applying very specific assumptions which select against unique structural characteristics. For this reason, data agnostic tools able to learn from presented data can be very useful with new species or with novel datasets. We have developed IgMAT, which utilises a reduced amino acid alphabet, that incorporates multiple HMM alignments into a single consensus to automatically annotate immunoglobulin sequences from most organisms. Additionally, the software allows the incorporation of user defined databases to better represent the species and/or antibody class of interest. To demonstrate the accuracy and utility of IgMAT, we present analysis of sequences extracted from structural data and immunoglobulin sequence datasets from several different species. IgMAT is fully open-sourced and freely available on GitHub (https://github.com/TPI-Immunogenetics/igmat) for download under GPLv3 license. It can be used as a CLI application or as a python module to be integrated in custom scripts. The online version contains supplementary material available at 10.1186/s12859-023-05624-2.
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影响因子：
3.6
作者：
Manso, Taciana Conceicao;Groenner-Penna, Michele;Felicori, Liza F.
通讯作者：
Felicori, Liza F.
影响因子：
5.8
作者：
Olimpieri, Pier Paolo;Chailyan, Anna;Marcatili, Paolo
通讯作者：
Marcatili, Paolo
影响因子：
5.8
作者：
Dunbar, James;Deane, Charlotte M.
通讯作者：
Deane, Charlotte M.
影响因子：
7.3
作者：
Li, Kun;Wang, Sheng;Liu, Zaixin
通讯作者：
Liu, Zaixin
影响因子：
14.9
作者：
Giudicelli, W;Chaume, D;Lefranc, MP
通讯作者：
Lefranc, MP