Document Type
Article
Publication Date
1-1-2021
Publication Title
Microbial Genomics
Volume
7
Issue
10
Pages
1-6
Publisher Name
Microbiology Society
Abstract
Bacterial genomes often reflect a bias in the usage of codons. These biases are often most notable within highly expressed genes. While deviations in codon usage can be attributed to selection or mutational biases, they can also be functional, for example controlling gene expression or guiding protein structure. Several different metrics have been developed to identify biases in codon usage. Previously we released a database, CBDB: The Codon Bias Database, in which users could retrieve precalculated codon bias data for bacterial RefSeq genomes. With the increase of bacterial genome sequence data since its release a new tool was needed. Here we present the Dynamic Codon Biaser (DCB) tool, a web application that dynamically calculates the codon usage bias statistics of prokaryotic genomes. DCB bases these calculations on 40 different highly expressed genes (HEGs) that are highly conserved across different prokaryotic species. A user can either specify an NCBI accession number or upload their own sequence. DCB returns both the bias statistics and the genome’s HEG sequences. These calculations have several downstream applications, such as evolutionary studies and phage–host predictions. The source code is freely available, and the website is hosted at www.cbdb.info.
Identifier
85120929559 (Scopus)
Recommended Citation
Dehlinger, Brian; Jurss, Jared; Lychuk, Karson; and Putonti, Catherine. The Dynamic Codon Biaser: calculating prokaryotic codon usage biases. Microbial Genomics, 7, 10: 1-6, 2021. Retrieved from Loyola eCommons, Biology: Faculty Publications and Other Works, http://dx.doi.org/10.1099/MGEN.0.000663
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
