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SourceForge net codonw program
Codonw Program, supplied by SourceForge net, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/program+codonw/codonw+program/pmc11547030-230-1-6
Average 90 stars, based on 1 article reviews
codonw program - by Bioz Stars, 2026-09
90/100 stars

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Article Title: Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages
Article Snippet: The CodonW program ( https://sourceforge.net/projects/codonw/ ) was used to analyse codon bias (default parameters), and the ENC-plot was created using the R package to detect the effect of base composition on codon bias, with the standard curve calculated as ENC = 2 + GC3s + 29/[GC3s2 + (1—GC3s)2] [ , ].

Article Title: Molecular characterization, function, tissue differential expression, and single-nucleotide polymorphism of buffalo <i>TP53</i> gene
Article Snippet: The relative synonymous codon usage (RSCU) for CDS was analyzed using the CodonW (http://codonw. sourceforge.net/, last access: 6 February 2024) program.

Article Title: Phylogenomic analysis and dynamic evolution of chloroplast genomes of Clematis nannophylla
Article Snippet: Nucleotides A, T, C, and G were acquired using the CodonW program (version 1.4.2, available at https://sourceforge.net/projects/codonw/ ) .

Article Title: Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates.
Article Snippet: Identification of key sequence, expression and function related features of nucleic acid-sensing host proteins is of fundamental importance to understand the dynamics of pathogen-specific host responses.. To meet this objective, we considered toll-like receptors (TLRs), a representative class of membrane-bound sensor proteins, from 17 vertebrate species covering mammals, birds, reptiles, amphibians, and fishes in this comparative study.. We identified the molecular signatures of host TLRs that are responsible for sensing pathogen nucleic acids or other pathogen-associated molecular patterns (PAMPs), and potentially play important roles in host defence mechanism.

Article Title: The genetic evolution and codon usage pattern of severe fever with thrombocytopenia syndrome virus.
Article Snippet: COA was performed using CodonW program (http://sourceforge.net/projec ts/codonw, written by John Peden) (Peden, 1999) based on the RSCU values.

Article Title: Evolutionary perspectives and adaptation dynamics of human seasonal influenza viruses from 2009 to 2019: An insight from codon usage.
Article Snippet: The annually recurrent seasonal influenza viruses, namely, influenza A viruses (H1N1/pdm2009 and H3N2) and influenza B viruses, contribute substantially to human disease burden.. Elucidation of host adaptation, population dynamics and evolutionary patterns of these viruses contribute to better control of current epidemic situation and bolster efforts towards pandemic preparedness.. Present study has been addressed at unraveling the signatures of codon usage and dinucleotide distribution of these seasonal influenza viruses associating with their fitness and ongoing adaptive evolution in human population.

Article Title: Characterization, Codon Usage Pattern and Phylogenetic Implications of the Waterlily Aphid Rhopalosiphum nymphaeae (Hemiptera: Aphididae) Mitochondrial Genome
Article Snippet: The CodonW program downloaded from ( http://codonw.sourceforge.net , 9 July 2024) and CUSP (EMBOSS Explorer (bioinformatics.nl)) were used to obtain a series of codon usage bias indices, including the Enc value (effective number of codons), GC3 value (G+C content at the third positions of codons), etc.

Article Title: Genetic and codon usage bias analyses of major capsid protein gene in Ranavirus.
Article Snippet: The Ranavirus (one genus of Iridovidae family) is an emerging pathogen that infects fish, amphibian, and reptiles, and causes great economical loss and ecological threat to farmed and wild animals globally.. The major capsid protein (MCP) has been used as genetic typing marker and as target to design vaccines.. Herein, the codon usage pattern of 73 MCP genes of Ranavirus and Lymphocystivirus are studied by calculating effective number of codons (ENC), relative synonymous codon usage (RSCU), codon adaptation index (CAI), and relative codon deoptimization index (RCDI), and similarity index (SiD).



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