chem16S：用于探索基因组对环境的遗传适应性的群落水平化学指标。
chem16S: community-level chemical metrics for exploring genomic adaptation to environments.
机构信息
Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring of Ministry of Education, School of Geosciences and Info-Physics, Central South University, Changsha, Hunan 410083, China.
出版信息
Bioinformatics. 2023 Sep 2;39(9). doi: 10.1093/bioinformatics/btad564.
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.
摘要
chem16S 包将 16S rRNA 基因序列的分类与原核参考蛋白质组的氨基酸组成相结合，以生成群落参考蛋白质组。支持 RDP 分类器的分类或 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，以探索氧化还原、盐度和其他物理化学变量对群落水平蛋白质序列基因组适应的影响。
可用性和实现
chem16S 的开发托管在 https://github.com/jedick/chem16S。版本 1.0.0 可从 Comprehensive R Archive Network (CRAN) 免费获得，网址为 https://cran.r-project.org/package=chem16S。
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