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Codon usage bias in Physcomitrella patens. Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in coding DNA.A codon is a series of three nucleotides (a triplet) that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation (stop codons).
The Codon Adaptation Index (CAI) [1] is the most widespread technique for analyzing codon usage bias.As opposed to other measures of codon usage bias, such as the 'effective number of codons' (Nc), which measure deviation from a uniform bias (null hypothesis), CAI measures the deviation of a given protein coding gene sequence with respect to a reference set of genes.
Effective number of codons (abbreviated as ENC or Nc) is a measure to study the state of codon usage biases in genes and genomes. [1] The way that ENC is computed has obvious similarities to the computation of effective population size in population genetics . [ 2 ]
Statistics Menu consists of Nucleotide Composition, Nucleotide Pair Frequencies, Codon Usage, Amino Acid Composition, Use All Selected Sites, Use only Highlighted Sites, Display Results in Spreadsheet (Excel or Libre/Open Office), Display Results in Comma-Delimited (CSV), Display Result in Text Editor. [23]
This table is found in both DNA Codon Table and Genetic Code (And probably a few other places), so I'm pulling it out so it can be common. By default it's the DNA code (using the letter T for Thymine); use template parameter "T=U" to make it the RNA code (using U for Uracil). See also Template:Inverse codon table
Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS is an acronym for European Molecular Biology Open Software ...
The ORF Finder (Open Reading Frame Finder) [16] is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database. This tool identifies all open reading frames using the standard or alternative genetic codes.
The frequency of codons, also known as codon usage bias, can vary from species to species with functional implications for the control of translation. The codon varies by organism; for example, most common proline codon in E. coli is CCG, whereas in humans this is the least used proline codon. [53]