# Genetic Code Table
#
# Obtained from: http://www.ncbi.nlm.nih.gov/collab/FT/genetic_codes.html
# and: http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c
#
# Differences from the Standard Code: 
# 
#         Code 4         Standard
# 
#  UGA    Trp  W          Ter  *
# 
# 
# Alternative Initiation Codons: 
# 
# Trypanosoma: UUA, UUG, CUG
# Leishmania: AUU, AUA 
# Tertrahymena: AUU, AUA, AUG 
# Paramecium: AUU, AUA, AUG, AUC, GUG, GUA(?) 
# (Pritchard et al., 1990)
# 
# Systematic Range: 
# 
# Mycoplasmatales: Mycoplasma, Spiroplasma (Bove et al., 1989); 
# 
# Fungi: Emericella nidulans, Neurospora crassa, Podospora anserina,
# Acremonium (Fox, 1987), Candida parapsilosis (Guelin et al., 1991),
# Trichophyton rubrum (de Bievre and Dujon, 1992), Dekkera/Brettanomyces,
# Eeniella (Hoeben et al., 1993), and probably Ascobolus immersus,
# Aspergillus amstelodami, Claviceps purpurea, and Cochliobolus
# heterostrophus. 
# 
# Protozoa: Trypanosoma brucei, Leishmania tarentolae, Paramecium
# tetraurelia, Tetrahymena pyriformis and probably Plasmodium gallinaceum
# (Aldritt et al., 1989)]. 
# 
# Metazoa: Coelenterata (Ctenophora and Cnidaria) 
# 
# Comments: 
# 
# This code is also used for the kinetoplast DNA (maxicircles,
# minicircles).  Kinetoplasts are modified mitochondria (or their parts). 
# 
# This code is not used in the Acholeplasmataceae and plant-pathogenic
# mycoplasma-like organisms (MLO) (Lim and Sears, 1992)

Genetic Code [4]
  
Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
  
AAs  =   FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = --MM---------------M------------MMMM---------------M------------
Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
