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Volume 7, Issue 10

The Dynamic Codon Biaser: calculating prokaryotic codon usage biases Open Access

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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): codon bias , codon usage , Dynamic Codon Biaser and prokaryotes
Funding
This study was supported by the:
  • National Science Foundation (Award 1661357)
    • Principle Award Recipient: CatherinePutonti
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2021-10-26
2024-04-19
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The Dynamic Codon Biaser: calculating prokaryotic codon usage biases
M Gen 7, 000663 (2021); https://doi.org/10.1099/mgen.0.000663
/content/journal/mgen/10.1099/mgen.0.000663
/content/journal/mgen/10.1099/mgen.0.000663
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