SIMMAP offers 17 different genetic codes that selected for an analysis of molecular data. The codes are derived from the NCBI genetic code table, version 3.8. Currently, alternate start codons are not recognized in amino acid mappings (only those listed as "ncbieaa" are used). If you are uncertain about the NCBI coding see the description below.

Changing the Genetic Code

Changing the genetic code is simple (see window graphic below). Select the Data main menu item and choose Set Genetic Codes... and select the desired code using the pop-up button labelled Code:. The current genetic coding has changed so simply close the window.


Making the Genetic Code Persistent with SIMMAP Preferences

If your work involves a particular code you can set the desired code to be persistent by altering the preferences. To do this select the SIMMAP item in menu bar and choose Preferences.... This action will open the Preferences window. If not already selected, select the Characters tab. Next, select the desired item in the pop up button, Genetic Code:. Finally, mouse click the Save button and in the future this will be the default genetic code.

NCBI Genetic Code Table, Version 3.8

**************************************************************************
-- This is the NCBI genetic code table
-- Initial base data set from Andrzej Elzanowski while at PIR International
-- Addition of Eubacterial and Alternative Yeast by J.Ostell at NCBI
-- Base 1-3 of each codon have been added as comments to facilitate
-- readability at the suggestion of Peter Rice, EMBL
-- Later additions by Taxonomy Group staff at NCBI
--
-- Version 3.8
-- Added GTG start to Echinoderm mitochondrial code, code 9
--
-- Version 3.7
-- Added code 23 Thraustochytrium mitochondrial code
-- formerly OGMP code 93
-- submitted by Gertraude Berger, Ph.D.
--
-- Version 3.6
-- Added code 22 TAG-Leu, TCA-stop
-- found in mitochondrial DNA of Scenedesmus obliquus
-- submitted by Gertraude Berger, Ph.D.
-- Organelle Genome Megasequencing Program, Univ Montreal
--
-- Version 3.5
-- Added code 21, Trematode Mitochondrial
-- (as deduced from: Garey & Wolstenholme,1989; Ohama et al, 1990)
-- Added code 16, Chlorophycean Mitochondrial
-- (TAG can translated to Leucine instaed to STOP in chlorophyceans
-- and fungi)
--
-- Version 3.4
-- Added CTG,TTG as allowed alternate start codons in Standard code.
-- Prats et al. 1989, Hann et al. 1992
--
-- Version 3.3 - 10/13/95
-- Added alternate intiation codon ATC to code 5
-- based on complete mitochondrial genome of honeybee
-- Crozier and Crozier (1993)
--
-- Version 3.2 - 6/24/95
-- Code Comments
-- 10 Alternative Ciliate Macronuclear renamed to Euplotid Macro...
-- 15 Bleharisma Macro.. code added
-- 5 Invertebrate Mito.. GTG allowed as alternate initiator
-- 11 Eubacterial renamed to Bacterial as most alternate starts
-- have been found in Achea
--
--
-- Version 3.1 - 1995
-- Updated as per Andrzej Elzanowski at NCBI
-- Complete documentation in NCBI toolkit documentation
-- Note: 2 genetic codes have been deleted
--
-- Old id Use id - Notes
--
-- id 7 id 4 - Kinetoplast code now merged in code id 4
-- id 8 id 1 - all plant chloroplast differences due to RNA edit
--
*************************************************************************

Genetic-code-table ::= {
{
name "Standard" ,
name "SGC0" ,
id 1 ,
ncbieaa "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "---M---------------M---------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Vertebrate Mitochondrial" ,
name "SGC1" ,
id 2 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG",
sncbieaa "--------------------------------MMMM---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Yeast Mitochondrial" ,
name "SGC2" ,
id 3 ,
ncbieaa "FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "----------------------------------MM----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate
Mitochondrial; Mycoplasma; Spiroplasma" ,
name "SGC3" ,
id 4 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "--MM---------------M------------MMMM---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Invertebrate Mitochondrial" ,
name "SGC4" ,
id 5 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG",
sncbieaa "---M----------------------------MMMM---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear" ,
name "SGC5" ,
id 6 ,
ncbieaa "FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "-----------------------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Echinoderm Mitochondrial" ,
name "SGC8" ,
id 9 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
sncbieaa "-----------------------------------M---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Euplotid Nuclear" ,
name "SGC9" ,
id 10 ,
ncbieaa "FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "-----------------------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Bacterial and Plant Plastid" ,
id 11 ,
ncbieaa "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "---M---------------M------------MMMM---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Alternative Yeast Nuclear" ,
id 12 ,
ncbieaa "FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "-------------------M---------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Ascidian Mitochondrial" ,
id 13 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG",
sncbieaa "-----------------------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
},
{
name "Flatworm Mitochondrial" ,
id 14 ,
ncbieaa "FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
sncbieaa "-----------------------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Blepharisma Macronuclear" ,
id 15 ,
ncbieaa "FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "-----------------------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Chlorophycean Mitochondrial" ,
id 16 ,
ncbieaa "FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "-----------------------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Trematode Mitochondrial" ,
id 21 ,
ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
sncbieaa "-----------------------------------M---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Scenedesmus obliquus mitochondrial" ,
id 22 ,
ncbieaa "FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "-----------------------------------M----------------------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
} ,
{
name "Thraustochytrium mitochondrial code" ,
id 23 ,
ncbieaa "FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
sncbieaa "--------------------------------M--M---------------M------------"
-- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
-- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
-- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
}
}