Genetic codes and other repeated ACD lists

Peter Rice pmr at
Fri Apr 8 13:18:42 UTC 2005

Dr J.C. Ison wrote:

> Peter Rice wrote:
>>Thanks. Domainatrix I assume. Which ones? I will take a look and see how they
>>fit in.
> The newly committed matgen3d and siggenlig, which both take an "environment 
> definition" (amino acid 3D environment) from a list.
> At the moment, the environemnts names are "Env1", "Env2" etc but would get more 
> meaningful names once the definitions themselves are more settled (pending 
> further research on which ones are most useful).

The genetic code format is very simple - the name, a space and the value with 
leading spaces and #commented lines ignored (this is the EGC.index file for an 
"@EGC.index" resource value)

  0 Standard with AUG start only
  1 Standard
  2 Vertebrate mitochondrial
  3 Yeast mitochondrial
  4 Mold, Protozoan, and Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
  5 Invertebrate Mitochondrial
  6 Ciliate, Dasycladacean and Hexamita Nuclear
# 7 *Kinetoplast code now merged in code id 4
# 8 *Plant chloroplast all differences due to RNA edit use code id 1
  9 Echinoderm and Flatworm Mitochondrial
10 Euplotid Nuclear
11 Bacterial and Plant Plastid
12 Alternative Yeast Nuclear
13 Ascidian Mitochondrial
14 Alternative Flatworm Mitochondrial
15 Blepharisma Nuclear
16 Chlorophycean Mitochondrial
#17 Never defined
#18 Never defined
#19 Never defined
#20 Never defined
21 Trematode Mitochondrial
22 Scenedesmus obliquus Mitochondrial
23 Thraustochytrium Mitochondrial

> They could simply acdprettyify the files as described in your prev. email 
> before parsing, so they wouldn't need to do any new coding.

But maybe not those who use the ACD file at run time :-)



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