Bioinformatics Toolbox™

geneticcode - Return nucleotide codon to amino acid mapping for genetic code

Syntax

Map = geneticcode Map = geneticcode(GeneticCode)

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.

Return Values

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

Description

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

Map = geneticcode(GeneticCode) returns a structure containing the mapping of nucleotide codons to amino acids 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.

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 mapping of nucleotide codons to amino acids for the Flatworm Mitochondrial genetic code.

wormmap = geneticcode('Flatworm Mitochondrial');

References

[1] NCBI Web page describing genetic codes:

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