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, ...'Ambiguous', AmbiguousValue, ...)
CodonFreq = codonbias(SeqNT, ...'Pie', PieValue, ...)

Input 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, fastqread, 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).
AmbiguousValue	String specifying how to treat codons containing ambiguous nucleotide characters (R, Y, K, M, S, W, B, D, H, V, or N). Choices are: 'ignore' (default) — Skips codons containing ambiguous characters 'prorate' — Counts codons containing ambiguous characters and distributes them proportionately in the appropriate codon fields. For example, the counts for the codon ART are distributed evenly between the AAT and AGT fields. 'warn' — Skips codons containing ambiguous characters and displays a warning.
PieValue	Controls the creation of a figure of 20 pie charts, one for each amino acid. Choices are true or false (default).

Output Arguments

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, ...'Ambiguous', AmbiguousValue, ...) specifies how to treat codons containing ambiguous nucleotide characters. Choices are 'ignore' (default), 'prorate', and 'warn'.

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

1. 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');

2. 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.

   

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

   cb.Ala
   
   ans = 
   
       Codon: {'GCA' "GCC' "GCG' 'GCT'}
        Freq: [0.1600 0.3867 0.2533 02000]   

See Also

aminolookup | codoncount | geneticcode | nt2aa

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