chem16S：用于探索基因组对环境适应的社区级化学指标。

IF 4.4 3区生物学 Q1 BIOCHEMICAL RESEARCH METHODS Bioinformatics Pub Date : 2023-09-02 DOI:10.1093/bioinformatics/btad564

Jeffrey M Dick, Xun Kang

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引用次数: 0

摘要

摘要：chem16S包将16S rRNA基因序列的分类分类与原核参考蛋白质组的氨基酸组成相结合，生成群落参考蛋白质组。支持RDP分类器中的分类或phyloseq R包创建的数据对象。用户可以计算和可视化各种化学指标，以便在群落水平上探索氧化还原、盐度和其他物理化学变量对蛋白质序列基因组适应的影响。可用性和实施：chem16S的开发位于https://github.com/jedick/chem16S.1.0.0版本可从综合R档案网络（CRAN）免费获得，网址为https://cran.r-project.org/package=chem16S.

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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chem16S: community-level chemical metrics for exploring genomic adaptation to environments.

Summary: The chem16S package combines taxonomic classifications of 16S rRNA gene sequences with amino acid compositions of prokaryotic reference proteomes to generate community reference proteomes. Taxonomic classifications from the RDP Classifier or data objects created by the phyloseq R package are supported. Users can calculate and visualize a variety of chemical metrics in order to explore the effects of redox, salinity, and other physicochemical variables on the genomic adaptation of protein sequences at the community level.

Availability and implementation: Development of chem16S is hosted at https://github.com/jedick/chem16S. Version 1.0.0 is freely available from the Comprehensive R Archive Network (CRAN) at https://cran.r-project.org/package=chem16S.

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来源期刊

Bioinformatics 生物-生化研究方法

CiteScore

11.20

自引率

5.20%

发文量

753

审稿时长

2.1 months

期刊介绍： The leading journal in its field, Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers. Its main focus is on new developments in genome bioinformatics and computational biology. Two distinct sections within the journal - Discovery Notes and Application Notes- focus on shorter papers; the former reporting biologically interesting discoveries using computational methods, the latter exploring the applications used for experiments.