Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA.
Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA.
Microb Genom. 2021 Oct;7(10). doi: 10.1099/mgen.0.000663.
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.
细菌基因组通常反映出密码子使用的偏向性。这些偏向性在高表达基因中最为明显。虽然密码子使用的偏差可以归因于选择或突变偏向，但它们也可能是功能性的，例如控制基因表达或指导蛋白质结构。已经开发了几种不同的指标来识别密码子使用的偏向性。之前，我们发布了一个数据库 CBDB：密码子偏向数据库，用户可以在其中检索细菌 RefSeq 基因组的预计算密码子偏向数据。自发布以来，随着细菌基因组序列数据的增加，需要一个新的工具。在这里，我们介绍了动态密码子偏向计算器（DCB）工具，这是一个用于动态计算原核生物基因组密码子使用偏向性统计的 Web 应用程序。DCB 基于 40 种在不同原核生物物种中高度保守的高度表达基因（HEGs）来进行这些计算。用户可以指定 NCBI 访问号或上传自己的序列。DCB 返回偏倚统计数据和基因组的 HEG 序列。这些计算有几个下游应用，例如进化研究和噬菌体-宿主预测。源代码是免费提供的，网站托管在 www.cbdb.info 上。
