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

Syntax

Input 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.

Output Arguments

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

See Also

aa2nt | aminolookup | baselookup | codonbias | dnds | dndsml | nt2aa | revgeneticcode | seqshoworfs | seqtool

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