doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.

IF 5.4 Bioinformatics (Oxford, England) Pub Date : 2025-02-04 DOI:10.1093/bioinformatics/btaf043

Fabricio Almeida-Silva, Yves Van de Peer

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Abstract

Summary: Gene and genome duplications are major evolutionary forces that shape the diversity and complexity of life. However, different duplication modes have distinct impacts on gene function, expression, and regulation. Existing tools for identifying and classifying duplicated genes are either outdated or not user-friendly. Here, we present doubletrouble, an R/Bioconductor package that provides a comprehensive and robust framework for analyzing duplicated genes from genomic data. doubletrouble can detect and classify gene pairs as derived from six duplication modes (segmental, tandem, proximal, retrotransposon-derived, DNA transposon-derived, and dispersed duplications), calculate substitution rates, detect signatures of putative whole-genome duplication events, and visualize results as publication-ready figures. We applied doubletrouble to classify the duplicated gene repertoire in 822 eukaryotic genomes, and results were made available through a user-friendly web interface.

Availability and implementation: doubletrouble is available on Bioconductor (https://bioconductor.org/packages/doubletrouble), and the source code is available in a GitHub repository (https://github.com/almeidasilvaf/doubletrouble). doubletroubledb is available online at https://almeidasilvaf.github.io/doubletroubledb/.

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doubletrouble：一个R/Bioconductor软件包，用于基因和基因组复制的识别、分类和分析。

基因和基因组的复制是形成生命多样性和复杂性的主要进化力量。然而，不同的复制模式对基因的功能、表达和调控有不同的影响。现有的识别和分类重复基因的工具要么过时，要么不方便用户使用。在这里，我们提出了doubletrouble，这是一个R/Bioconductor软件包，它提供了一个全面而强大的框架，用于从基因组数据中分析重复基因。doubletrouble可以检测和分类来自六种复制模式的基因对（片段复制、串联复制、近端复制、反转录转座子衍生、DNA转座子衍生和分散复制），计算替代率，检测假定的全基因组复制事件的特征，并将结果可视化为可发表的数据。我们应用双麻烦对822个真核生物基因组的重复基因库进行分类，并通过用户友好的web界面提供结果。可用性和实现：doubletrouble可在Bioconductor （https://bioconductor.org/packages/doubletrouble）上获得，源代码可在GitHub存储库（https://github.com/almeidasilvaf/doubletrouble）中获得。补充数据可在Bioinformatics online和https://github.com/almeidasilvaf/doubletrouble_paper上获得。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Bioinformatics (Oxford, England)

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