An analysis of the phenomenon of codon bias

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An analysis of the phenomenon of codon bias

This program is designed to perform various tasks that are of use for evaluating codon usage in a set of genes. You can get it to do some simple things like calculate the number of observations of a particular codon in a gene.

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Or you can do the same thing for the combined dataset. You can also look at amino acid usage frequencies again for each gene or for the dataset as a whole. The program also produces a distance matrix based on the similarity of codon usage in genes. Although it is popular to say that an organism has a particular codon usage, it is now known that an organisms genes might have more than one codon usage pattern and it is usually only by using a multivariate analysis method that it is possible to ascertain the kinds of variation contained within the data.

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Read in a Fasta-formatted file. The FastA or Pearson format is the simplest method of representing molecular sequence data. The sequence data begins on the next line. If your data is in a different format, you can use Readseq by Don Gilbert to reformat the data into FastA format.

It does a limited amount of checking of the sequence format, but if you, the user does not ensure that the format requirements which are not very stringent are met, it could do some funny things.

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The limit on sequence length at the moment is 15, bp and the limit on number of sequences is 5, It is hoped that future development work will mean that there will not be any explicit restriction on sequence number or length.

The purpose of this function is to calculate the Number N of times a particular codon is observed in a gene or set of genes and also to calculate the Relative Synonymous Codon Usage RSCU values for the dataset.

An analysis of the phenomenon of codon bias

RSCU values are the number of times a particular codon is observed, relative to the number of times that the codon would be observed in the absence of any codon usage bias.

In the absence of any codon usage bias, the RSCU value would be 1. The program adds up the total number of times that the codons for a particular amino acid are observed depending on the amino acid, this might be 2,3,4 or 6 differnet codons. It then divides this number by the number of codons for the amino acid 2,3,4 or 6this gives the expected number of times that the codons should be observed.

Then for each codon, the frequency of observation is divided by the expected frequency. Sometimes the observed frequency will be greater than the expected frequency RSCU value greater than 1.

The calculation is as follows: It makes the codon usage value independent of amino acid composition of the sequences and identifies when a codon is being used more frequently than expected and when it is being used less frequently than expected.

Nc The Effective Number of codons measure is a way of analysing how biased a gene is in terms of its codon usage.

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Nc values range from 61 for a gene that tends to use all codons with equal frequency to 20 for a gene that is effectively using only a single codon for each amino acid. There is a relationship between Nc and the base composition of a gene with genes that have more biased base compositions being expected to have lower Nc values.

What is usually of interest are Nc values that are lower than might be dictated by the base composition of the gene. This might be taken as evidence that there is some kind of selective pressure on the gene to use a smaller subset of codons.

An analysis of the phenomenon of codon bias

Optimal codons are those that correspond to the major abundance tRNA for that amino acid. In such circumstances, there could be a selective pressure to use a particular codon that corresponds to this tRNA.The effect of base substitutions, or point mutations, on the messenger-RNA codon AUA, which codes for the amino acid isoleucine.


Substitutions (red letters) at the first, second, or third position in the codon can result in nine new codons corresponding to six different amino acids in addition to isoleucine itself. Most amino acids are encoded by two to six synonymous codons. Preferential use of certain synonymous codons, a phenomenon called codon usage bias, was found in all genomes.

RSCU values are the number of times a particular codon is observed, relative to the number of times that the codon would be observed in the absence of any codon usage bias.

In the absence of any codon usage bias, the RSCU value would be Studies of codon usage have determined that several factors may influence codon usage patterns, including mutational bias and natural selection.

Analysis of codon usage patterns sheds light on the molecular biology of gene regulation, gene expression, secondary protein structure, selective transcription, and the external environment. The genetic code is the set of rules used by living cells to translate information encoded within genetic material (DNA or mRNA sequences) into barnweddingvt.comation is accomplished by the ribosome, which links amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time.

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Codon usage bias - an overview | ScienceDirect Topics