ArticleBMC research notes2010
RCDI/eRCDI: a web-server to estimate codon usage deoptimization.
Article in BMC research notes, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
50 citing papers in PubMed.
- Analysis of Codon Usage Bias in theThe Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale · 2026Article
- Codon usage bias of low-risk human papillomavirus types 6 and 11.Antonie van Leeuwenhoek · 2025Article
- Mapping evolutionary paradigm of Oropouche virus driven by dinucleotide bias and context-dependent codon bias.Virulence · 2025Article
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- Decoding codon usage in human papillomavirus type 59.Virus genes · 2025Article
- The Incidence and Genetic Analysis of Two Betaflexiviruses Capillovirus alphavii and Tepovirus tafpruni in Iran.The plant pathology journal · 2025Article
- Comprehensive analysis of the codon usage patterns in the polyprotein coding sequences of the honeybee viruses.Frontiers in veterinary science · 2025Article
- Genetic and codon usage analyses reveal the evolution of the seoul virus.Frontiers in genetics · 2025Article
- Comprehensive Analysis of Codon Usage Bias in Human Papillomavirus Type 51.Polish journal of microbiology · 2024Article
- Comprehensive Genomics Investigation of Neboviruses Reveals Distinct Codon Usage Patterns and Host Specificity.Microorganisms · 2024Article
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- Phylogenetic Analysis and Codon Usage Bias Reveal the Base of Feline and Canine Chaphamaparvovirus for Cross-Species Transmission.Animals : an open access journal from MDPI · 2023Article
- Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts.Pathogens (Basel, Switzerland) · 2023Article
- Article
- Vaccinia Virus Attenuation by Codon Deoptimization of the A24R Gene for Vaccine Development.Microbiology spectrum · 2022Article
- Article
- A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry.Journal of bacteriology · 2022Article
- Codon Usage of Hepatitis E Viruses: A Comprehensive Analysis.Frontiers in microbiology · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe Relative Codon Deoptimization Index (RCDI) was developed by Mueller et al. (2006) as measure of codon deoptimization by comparing how similar is the codon usage of a gene and the codon usage of a reference genome.
findingsRCDI/eRCDI is a web application server that calculates the Relative Codon Deoptimization Index and a new expected value for the RCDI (eRCDI). The RCDI is used to estimate the similarity of the codon frequencies of a specific gene in comparison to a given reference genome. The eRCDI is determined by generating random sequences with similar G+C and amino acid composition to the input sequences and may be used as an indicator of the significance of the RCDI values. RCDI/eRCDI is freely available at http://genomes.urv.cat/CAIcal/RCDI.
conclusionsThis web server will be a useful tool for genome analysis, to understand host-virus phylogenetic relationships or to infer the potential host range of a virus and its replication strategy, as well as in experimental virology to ease the step of gene design for heterologous protein expression.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.