GenRCA: a user-friendly rare codon analysis tool for comprehensive evaluation of codon usage preferences based on coding sequences in genomes.
Codon usage
Gene design
Protein expression
Rare codon analysis
Journal
BMC bioinformatics
ISSN: 1471-2105
Titre abrégé: BMC Bioinformatics
Pays: England
ID NLM: 100965194
Informations de publication
Date de publication:
27 Sep 2024
27 Sep 2024
Historique:
received:
20
12
2023
accepted:
17
09
2024
medline:
28
9
2024
pubmed:
28
9
2024
entrez:
28
9
2024
Statut:
epublish
Résumé
The study of codon usage bias is important for understanding gene expression, evolution and gene design, providing critical insights into the molecular processes that govern the function and regulation of genes. Codon Usage Bias (CUB) indices are valuable metrics for understanding codon usage patterns across different organisms without extensive experiments. Considering that there is no one-fits-all index for all species, a comprehensive platform supporting the calculation and analysis of multiple CUB indices for codon optimization is greatly needed. Here, we release GenRCA, an updated version of our previous Rare Codon Analysis Tool, as a free and user-friendly website for all-inclusive evaluation of codon usage preferences of coding sequences. In this study, we manually reviewed and implemented up to 31 codon preference indices, with 65 expression host organisms covered and batch processing of multiple gene sequences supported, aiming to improve the user experience and provide more comprehensive and efficient analysis. Our website fills a gap in the availability of comprehensive tools for species-specific CUB calculations, enabling researchers to thoroughly assess the protein expression level based on a comprehensive list of 31 indices and further guide the codon optimization.
Sections du résumé
BACKGROUND
BACKGROUND
The study of codon usage bias is important for understanding gene expression, evolution and gene design, providing critical insights into the molecular processes that govern the function and regulation of genes. Codon Usage Bias (CUB) indices are valuable metrics for understanding codon usage patterns across different organisms without extensive experiments. Considering that there is no one-fits-all index for all species, a comprehensive platform supporting the calculation and analysis of multiple CUB indices for codon optimization is greatly needed.
RESULTS
RESULTS
Here, we release GenRCA, an updated version of our previous Rare Codon Analysis Tool, as a free and user-friendly website for all-inclusive evaluation of codon usage preferences of coding sequences. In this study, we manually reviewed and implemented up to 31 codon preference indices, with 65 expression host organisms covered and batch processing of multiple gene sequences supported, aiming to improve the user experience and provide more comprehensive and efficient analysis.
CONCLUSIONS
CONCLUSIONS
Our website fills a gap in the availability of comprehensive tools for species-specific CUB calculations, enabling researchers to thoroughly assess the protein expression level based on a comprehensive list of 31 indices and further guide the codon optimization.
Identifiants
pubmed: 39333857
doi: 10.1186/s12859-024-05934-z
pii: 10.1186/s12859-024-05934-z
doi:
Substances chimiques
Codon
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
309Informations de copyright
© 2024. The Author(s).
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