diff --git a/etc/options b/etc/options index 8f290f80def2d8f5465bf939a0dc130186315985..35355efd705e5ed8e38947060e576e65658f3f92 100644 --- a/etc/options +++ b/etc/options @@ -2,7 +2,7 @@ # (Note that comment lines start with a hash (#) symbol) -# $Header: //tmp/pathsoft/artemis/etc/options,v 1.14 2005-01-12 10:37:28 tjc Exp $ +# $Header: //tmp/pathsoft/artemis/etc/options,v 1.15 2005-01-12 13:49:43 tjc Exp $ # This file should contain option settings that look like this: # @@ -39,67 +39,15 @@ direct_edit = yes # This setting controls which set of codons will be used for start codons. # This can be changed from the options menu. -# There are two possible settings: eukaryote or prokaryote -organism_type = eukaryote +# Give the translation table number. +# +genetic_code_default = 1 # This option gives the bases of the possible start codons eukaryotic_start_codons = atg prokaryotic_start_codons = atg gtg ttg -# The translation_table option is used to lookup codon translations. The -# table must have exactly 64 entries, and there is one entry for each codon. -# The entries should appear in this order: -# TTT, TTC, TTA, TTG, -# TCT, TCC, ..., -# ... - -# this is the default table: -# -# translation_table = \ -# f f l l \ -# s s s s \ -# y y # + \ -# c c * w \ -# \ -# l l l l \ -# p p p p \ -# h h q q \ -# r r r r \ -# \ -# i i i m \ -# t t t t \ -# n n k k \ -# s s r r \ -# \ -# v v v v \ -# a a a a \ -# d d e e \ -# g g g g - -# this is the eukaryotic mitochondrial table: -# -# translation_table = \ -# f f l l \ -# s s s s \ -# y y * * \ -# c c w w \ -# \ -# l l l l \ -# p p p p \ -# h h q q \ -# r r r r \ -# \ -# i i m m \ -# t t t t \ -# n n k k \ -# s s * * \ -# \ -# v v v v \ -# a a a a \ -# d d e e \ -# g g g g - # # Genetic Codes : # http://www3.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG1 @@ -131,6 +79,12 @@ genetic_codes = \ Scenedesmus_Obliquus_Mitochondrial \ Thraustochytrium_Mitochondrial +# The translation_table option is used to lookup codon translations. The +# table must have exactly 64 entries, and there is one entry for each codon. +# The entries should appear in this order: +# TTT, TTC, TTA, TTG, +# TCT, TCC, ..., +# ... # 1. standard code (default) translation_table_1 = \