The CodonW application was designed to be a package for codon usage analysis. It was designed to simplify Multivariate Analysis (MVA) of codon usage. The MVA method employed in CodonW is correspondence analysis (COA) (the most popular MVA method for codon usage analysis). CodonW can generate a COA for codon usage, relative synonymous codon usage or amino acid usage. Additional analyses of codon usage include investigation of optimal codons, codon and dinucleotide bias, and/or base composition. CodonW also has the capacity to analysis sequences encoded by genetic codes other than the universal code.
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CodonW Product Key is a highly portable program based on the classical MVA analysis methods and algorithms pioneered by Prof. F.R. Thompson and his colleagues, and in particular, the EST-COA method. The MVA methods can be used to study both the main and the relative synonymous codon usage (RSH), and to compare genome sequences. CodonW can be used to analyze multiple DNA sequences of the same species as well as different sequences of the same gene. The program is available as an Excel add-in, and as a VB 6 application. Both versions can work with DNA sequences of length up to 2 GB, or even longer. CodonW Excel Add-in: The CodonW add-in was designed to work with the Excel 2000 and greater. All basic MVA methods are included in the Excel package: 2D correspondence analysis, principal component analysis, stability analysis, and multiple correspondence analysis (MCA). Most of these methods are also available as stand-alone calculations in the CodonW program. This is what makes CodonW one of the most flexible tools available for codon usage analysis. CodonW VB6 Application: The application was developed to work with the Visual Basic 6 on Microsoft Windows. The basic MVA methods are included in the application. CodonW has a large number of additional features, including the capacity to analyze DNA sequences with different codon assignments. CodonW Windows Examples (direct link to the VFBOOT.EXE file for CodonW): 1. ENCODON(SEQUENCE) Input : a DNA sequence encoded in a particular genetic code. Output: Y1 = raw ENCODON(SEQUENCE) Y2 = ENCODON(SEQUENCE)-EFLAG 3. ENCODON(SEQUENCE) Input : a DNA sequence encoded in a particular genetic code. Output: Y1 = ENCODON(SEQUENCE)-YAS Y2 = ENCODON(SEQUENCE)-YFLAG 4. ENCODON(SEQUENCE)-DIST-R Input : a DNA sequence encoded in a particular genetic code. Output: Y1 = ENCODON(SEQUENCE)-DIST-R Y2 = DIST-R- 5. ENCODON(SEQUENCE)-DIST-R Input : a
CodonW is a graphical application for codon usage analyses in which the relative usage of each of the 64 codons in the standard genetic code is graphically represented, in a grid, by its usage in one or more mRNAs. Each codon is identified by a numeric identifier, the x-coordinate of its position in the grid, and a color (one of the 256 possible colors, with an intensity value) which corresponds to the relative frequency of occurrence of that codon in all the mRNAs being analyzed. Thus, an individual gene can be viewed as a point in a four-dimensional space spanned by the three coordinates (1st, 2nd and 3rd) and the 256 colors. Codon usage analysis is a powerful tool for: 1) detecting genes from foreign organisms in gene databases and in the tree of life, 2) characterizing the genetic code, 3) identifying cellular mechanisms of gene expression, 4) designing synthetic genes for protein production, and 5) studying the evolution of gene sequences, by comparing a new sequence to an already-sequenced one. Codon usage analysis with CodonW is performed in two steps. First, a user imports a set of sequences (usually one or more genomes), and the 64 codons are identified in the individual sequences. Then, a user can use a graphical tool to select, for each of the codons, the cells in a grid that are to be displayed by the program. The user then prepares a text file, which is subsequently uploaded to a web server which implements the analysis. This is the first letter of the twenty-sixth edition of “The Codon Usage Database,” downloaded Oct. 15, 1998 from the URL It is the fifth edition of “The Codon Usage Database,” which was downloaded from the URL on July 6, 2002. The twenty-eighth edition of “Codon Usage Database,” downloaded Oct. 15, 1998 from the URL The twenty-eighth edition of “The Codon Usage Database,” downloaded on November 3, 1998 from the URL 2f7fe94e24
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CodonW is a Batch application developed by WatsonWare. It can be used as stand-alone PC application with a simple graphical user interface (GUI) or as a console application. It was developed to support the codon analysis and optimization. The application have the following features : • Sequences (User can paste or upload either single or multiple sequences) • Various options to set the input sequences : – A number of sequences (from 1 to 10000) – Selected sequences (from one or more files) – Random sequences – Number of sequences – Segregated sequences – Any sequences as reference files – Set input files as template sequence – History of input sequences (removed sequences) – Taxonomical tree of the input sequences – Bioinformatic analysis (protein families) – Database of mapping between annotations of input sequences – Alignment of selected sequences – Set the coding frame and the ORF for the sequences (biological or not) – Set the codon usage rules : make a decision of the best of all – Set the wobble rule • Various graphical outputs : – graphical view of calculated codon usage – graphical views of optimal, sub-optimal, and rare codons – graphical view of codon usage with a CCA3 – graphical view of optimal codons : some graphical view of the optimal codons based on a point plot of the frequency of codon usage in a sliding window of 50 codons – graphical views of other analysis (bias, etc.) – graphical view of «best» codons – graphical view of «worst» codons (for single sequences only) • Sequence statistics: – statistical view of frequency of codon usage – statistical view of statistical parameters : variance of codon usage and GC contents – statistical view of correspondence analysis (COA) – statistical view of optimal codons for the given sequences – statistical view of biases : over- or under-represented codon at the 3’ or 5’-end of the sequences – Statistical view of rare codons – statistical view of best codons : for a set of sequences only – statistical view of worst codons – statistical view of optimal codons for a set of sequences only – graphical view of codon usage for each amino acid • Search sequences in the UniProtKB and SWISSPROT databases
What’s New In CodonW?
CodonW is a simple GUI interface for COA.COA is the most popular MVA method for codon usage analysis. CodonW performs a user-friendly COA, using the Jaccard Index as an input. All genes from a set of organisms, for example an alignment of all genes from your favorite genome, can be used as input for CodonW. The Jaccard Index is calculated as:JI(g,g1) = S(g,g1) / S(g) where g is an element of the compared lists g = [g1,…,gn], S(g) is the number of elements of the list g, and S(g,g1) is the number of elements that have both elements g and g1 as a common element. It is possible to compare two genomes with a pairwise-genome-alignment of the coding sequences. This is not necessary, because the whole genomes can be used as input for CodonW. Moreover, for the sake of clarity CodonW allows the addition of genomes without a pairwise-genome-alignment, as long as this list is parsed in the CodonW analysis. The Jaccard Index is used in CodonW.Jaccard Index is the most common index used for codon usage analysis. How to The table below shows how many elements in which element are present in the list of input sequences. If the list of input sequences is not given or not properly parsed in the CodonW analysis the complete list of sequences are analyzed. S(g,g1) = # of elements in list g and elements in list g1 S(g) = # elements in list g S(g,g1) = # elements in list g and elements in list g1 Description: Description: This entry stores the normalized values of RSCU of codon usage relative to the codon usage of the host genome. Description: If isGrammatical == 1 and length(sequences) > 1 then this entry stores the index of the codon usage and a list of sequences coding the codon. Description: RSCU(f) is the codon frequency of codon f divided by the sum of all codon frequencies. The distribution of codon
System Requirements For CodonW:
OS: Windows® 7, Windows® 8, Windows® 8.1, Windows® 10 (32/64-bit versions) Windows® 7, Windows® 8, Windows® 8.1, Windows® 10 (32/64-bit versions) Processor: 2 GHz processor with at least 1 GB RAM (4 GB recommended) 2 GHz processor with at least 1 GB RAM (4 GB recommended) Graphics: Microsoft DirectX 9 graphics hardware with a Shader Model 3.0 compliant graphics card Microsoft DirectX 9 graphics hardware with a Shader Model 3.