Cubar: a versatile package for codon usage bias analysis in R.

IF 5.1 3区生物学 Q2 GENETICS & HEREDITY

Genetics Pub Date : 2025-09-11 DOI:10.1093/genetics/iyaf191

Mengyue Liu, Bu Zi, Hebin Zhang, Hong Zhang

引用次数: 0

Abstract

Codon usage bias refers to the nonequal usage of synonymous codons. This phenomenon is fundamentally important in biology as it is jointly shaped by mutation, genetic drift, and natural selection, and influences translation rate, decoding accuracy, and mRNA stability. However, popular tools for codon usage bias analysis are not flexible nor efficient enough and fail to incorporate recent advancements in this field. To address these issues, we developed the Codon Usage Bias Analysis in R (cubar) package. Cubar is highly modular and can calculate common codon usage indexes in a user-friendly manner. In addition, it can perform sliding-window analyses of codon usage, assess differential usage between gene sets, and optimize user-provided genes based on the codon usage of a target organism. Furthermore, cubar is highly efficient and can analyze millions of coding sequences within a few minutes on a laptop.

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Cubar：一个通用的密码子使用偏差分析包。

密码子使用偏差是指同义密码子的不平等使用。这种现象在生物学中非常重要，因为它是由突变、遗传漂变和自然选择共同形成的，并影响翻译率、解码精度和mRNA稳定性。然而，目前流行的密码子使用偏差分析工具不够灵活，效率也不够高，未能结合该领域的最新进展。为了解决这些问题，我们开发了密码子使用偏差分析在R （cubar）包。Cubar是高度模块化的，可以以用户友好的方式计算常见密码子使用索引。此外，它还可以进行密码子使用的滑动窗口分析，评估基因集之间的差异使用情况，并根据目标生物的密码子使用情况优化用户提供的基因。此外，cubar非常高效，可以在几分钟内在笔记本电脑上分析数百万个编码序列。

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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来源期刊

Genetics GENETICS & HEREDITY-

CiteScore

6.90

自引率

6.10%

发文量

177

审稿时长

1.5 months

期刊介绍： GENETICS is published by the Genetics Society of America, a scholarly society that seeks to deepen our understanding of the living world by advancing our understanding of genetics. Since 1916, GENETICS has published high-quality, original research presenting novel findings bearing on genetics and genomics. The journal publishes empirical studies of organisms ranging from microbes to humans, as well as theoretical work. While it has an illustrious history, GENETICS has changed along with the communities it serves: it is not your mentor''s journal. The editors make decisions quickly – in around 30 days – without sacrificing the excellence and scholarship for which the journal has long been known. GENETICS is a peer reviewed, peer-edited journal, with an international reach and increasing visibility and impact. All editorial decisions are made through collaboration of at least two editors who are practicing scientists. GENETICS is constantly innovating: expanded types of content include Reviews, Commentary (current issues of interest to geneticists), Perspectives (historical), Primers (to introduce primary literature into the classroom), Toolbox Reviews, plus YeastBook, FlyBook, and WormBook (coming spring 2016). For particularly time-sensitive results, we publish Communications. As part of our mission to serve our communities, we''ve published thematic collections, including Genomic Selection, Multiparental Populations, Mouse Collaborative Cross, and the Genetics of Sex.