Bioinformatics Toolbox™

codonbias - Calculate codon frequency for each amino acid coded for in nucleotide sequence

Syntax

CodonFreq = codonbias(SeqNT) CodonFreq = codonbias(SeqNT, ...'GeneticCode', GeneticCodeValue, ...) CodonFreq = codonbias(SeqNT, ...'Frame', FrameValue, ...) CodonFreq = codonbias(SeqNT, ...'Reverse', ReverseValue, ...) CodonFreq = codonbias(SeqNT, ...'Pie', PieValue, ...)

Arguments

SeqNT

One of the following:

String of codes specifying a nucleotide sequence
Row vector of integers specifying a nucleotide sequence
MATLAB structure containing a Sequence field that contains a nucleotide sequence, such as returned by fastaread, emblread, getembl, genbankread, or getgenbank

Valid characters include A, C, G, T, and U.

codonbias does not count ambiguous nucleotides or gaps.

GeneticCodeValue

Integer or string specifying a genetic code number or code name from the table Genetic Code. Default is 1 or 'Standard'.

Tip If you use a code name, you can truncate the name to the first two letters of the name.

FrameValue

Integer specifying a reading frame in the nucleotide sequence. Choices are 1 (default), 2, or 3.

ReverseValue Controls the return of the codon frequency for the reverse complement sequence of the nucleotide sequence specified by SeqNT. Choices are true or false (default).

PieValue Controls the creation of a figure of 20 pie charts, one for each amino acid. Choices are true or false (default).

Return Values

CodonFreq MATLAB structure containing a field for each amino acid, each of which contains the associated codon frequencies as percentages.

Description

Many amino acids are coded by two or more nucleic acid codons. However, the probability that a specific codon (from all possible codons for an amino acid) is used to code an amino acid varies between sequences. Knowing the frequency of each codon in a protein coding sequence for each amino acid is a useful statistic.

CodonFreq = codonbias(SeqNT) calculates the codon frequency in percent for each amino acid coded for in SeqNT, a nucleotide sequence, and returns the results in CodonFreq, a MATLAB structure containing a field for each amino acid.

CodonFreq = codonbias(SeqNT, ...'PropertyName', PropertyValue, ...) calls codonbias with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:

CodonFreq = codonbias(SeqNT, ...'GeneticCode', GeneticCodeValue, ...) specifies a genetic code. Choices for GenetidCodeValue are an integer or string specifying a code number or code name from the table Genetic Code. If you use a code name, you can truncate the name to the first two characters of the name. Default is 1 or 'Standard'.

Tip If you use a code name, you can truncate the name to the first two letters of the name.

CodonFreq = codonbias(SeqNT, ...'Frame', FrameValue, ...) calculates the codon frequency in the reading frame specified by FrameValue, which can be 1 (default), 2, or 3.

CodonFreq = codonbias(SeqNT, ...'Reverse', ReverseValue, ...) controls the return of the codon frequency for the reverse complement of the nucleotide sequence specified by SeqNT. Choices are true or false (default).

CodonFreq = codonbias(SeqNT, ...'Pie', PieValue, ...) controls the creation of a figure of 20 pie charts, one for each amino acid. Choices are true or false (default).

Genetic Code

Code Number	Code Name
`1`	`Standard`
`2`	`Vertebrate Mitochondrial`
`3`	`Yeast Mitochondrial`
`4`	`Mold`, `Protozoan`, `Coelenterate Mitochondrial`, and `Mycoplasma/Spiroplasma`
`5`	`Invertebrate Mitochondrial`
`6`	`Ciliate`, `Dasycladacean`, and `Hexamita Nuclear`
`9`	`Echinoderm Mitochondrial`
`10`	`Euplotid Nuclear`
`11`	`Bacterial` and `Plant Plastid`
`12`	`Alternative Yeast Nuclear`
`13`	`Ascidian Mitochondrial`
`14`	`Flatworm Mitochondrial`
`15`	`Blepharisma Nuclear`
`16`	`Chlorophycean Mitochondrial`
`21`	`Trematode Mitochondrial`
`22`	`Scenedesmus Obliquus Mitochondrial`
`23`	`Thraustochytrium Mitochondrial`

Examples

Import a nucleotide sequence from the GenBank database into the MATLAB software. For example, retrieve the DNA sequence that codes for a human insulin receptor.
```
S = getgenbank('M10051');
```
Calculate the codon frequency for each amino acid coded for by the DNA sequence, and then plot the results.
```
cb = codonbias(S.Sequence,'PIE',true)
```
A figure with 20 pie charts for the 20 amino acids displays.

Get the codon frequency for the alanine (A) amino acid.