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

Jeffrey M Dick; Xun Kang

doi:10.1093/bioinformatics/btad564

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

Bioinformatics. 2023 Sep 2;39(9):btad564. doi: 10.1093/bioinformatics/btad564.

Authors

Jeffrey M Dick¹, Xun Kang¹

Affiliation

¹ 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.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence
Benchmarking*
Genomics
Proteome*
RNA, Ribosomal, 16S

Substances

Proteome
RNA, Ribosomal, 16S