Bioinformatics Toolbox™

revgeneticcode

Return reverse mapping (amino acid to nucleotide codon) for genetic code

Syntax

Map = revgeneticcode Map = revgeneticcode(GeneticCode) Map = revgeneticcode(..., 'Alphabet', AlphabetValue, ...) Map = revgeneticcode(..., 'ThreeLetterCodes', ThreeLetterCodesValue, ...)

Arguments

GeneticCode

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.

AlphabetValue

String specifying the nucleotide alphabet to use in the map. Choices are:

'DNA' (default) — Uses the symbols A, C, G, and T.
'RNA' — Uses the symbols A, C, G, and U.

ThreeLetterCodesValue

Controls the use of three-letter amino acid codes as field names in the return structure Map. Choices are true for three-letter codes or false for one-letter codes. Default is false.

Return Values

Map Structure containing the reverse mapping of amino acids to nucleotide codons for the standard genetic code. The Map structure contains a field for each amino acid.

Description

Map = revgeneticcode returns a structure containing the reverse mapping of amino acids to nucleotide codons for the standard genetic code. The Map structure contains a field for each amino acid.

Map = revgeneticcode(GeneticCode) returns a structure containing the reverse mapping of amino acids to nucleotide codons for the specified genetic code. GeneticCode is either:

An integer or string specifying a code number or code name from the table Genetic Code
The transl_table (code) number from the NCBI Web page describing genetic codes:
```
http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
```

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

Map = revgeneticcode(..., 'PropertyName', PropertyValue, ...) calls revgeneticcode 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:

Map = revgeneticcode(..., 'Alphabet', AlphabetValue, ...) specifies the nucleotide alphabet to use in the map. AlphabetValue can be 'DNA', which uses the symbols A, C, G, and T, or 'RNA', which uses the symbols A, C, G, and U. Default is 'DNA'.

Map = revgeneticcode(..., 'ThreeLetterCodes', ThreeLetterCodesValue, ...) controls the use of three-letter amino acid codes as field names in the return structure Map. ThreeLetterCodesValue can be true for three-letter codes or false for one-letter codes. Default is false.

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

Return the reverse mapping of amino acids to nucleotide codons for the Standard genetic code.

map = revgeneticcode

map = 

      Name: 'Standard'
         A: {'GCT'  'GCC'  'GCA'  'GCG'}
         R: {'CGT'  'CGC'  'CGA'  'CGG'  'AGA'  'AGG'}
         N: {'AAT'  'AAC'}
         D: {'GAT'  'GAC'}
         C: {'TGT'  'TGC'}
         Q: {'CAA'  'CAG'}
         E: {'GAA'  'GAG'}
         G: {'GGT'  'GGC'  'GGA'  'GGG'}
         H: {'CAT'  'CAC'}
         I: {'ATT'  'ATC'  'ATA'}
         L: {'TTA'  'TTG'  'CTT'  'CTC'  'CTA'  'CTG'}
         K: {'AAA'  'AAG'}
         M: {'ATG'}
         F: {'TTT'  'TTC'}
         P: {'CCT'  'CCC'  'CCA'  'CCG'}
         S: {'TCT'  'TCC'  'TCA'  'TCG'  'AGT'  'AGC'}
         T: {'ACT'  'ACC'  'ACA'  'ACG'}
         W: {'TGG'}
         Y: {'TAT'  'TAC'}
         V: {'GTT'  'GTC'  'GTA'  'GTG'}
     Stops: {'TAA'  'TAG'  'TGA'}
    Starts: {'TTG'  'CTG'  'ATG'}

Return the reverse mapping of amino acids to nucleotide codons for the Mold, Protozoan, Coelenterate Mitochondrial, and Mycoplasma/Spiroplasma genetic code, using the rna alphabet.
```
moldmap = revgeneticcode(4,'Alphabet','rna');
```
Return the reverse mapping of amino acids to nucleotide codons for the Flatworm Mitochondrial genetic code, using three-letter codes for the field names in the return structure.
```
wormmap = revgeneticcode('Flatworm Mitochondrial',...
                          'ThreeLetterCodes',true);
```

References

[1] NCBI Web page describing genetic codes:

http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c