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Commit b399351e authored by tjc's avatar tjc
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translation table mods

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2113 ee4ac58c-ac51-4696-9907-e4b3aa274f04
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...@@ -184,24 +184,18 @@ LINKEND="OPTIONS-PROKSTARTCODONS">. ...@@ -184,24 +184,18 @@ LINKEND="OPTIONS-PROKSTARTCODONS">.
</PARA> </PARA>
</SECT2> </SECT2>
<SECT2 ID="OPTIONS-EUKSTARTCODONS"> <SECT2 ID="OPTIONS-GENETICCODES">
<TITLE><LITERAL>eukaryotic_start_codons</LITERAL></TITLE> <TITLE><LITERAL>genetic_codes</LITERAL></TITLE>
<PARA> <PARA>
This option gives the bases of the possible start codons when &prog; is in This option gives the list of names of the available genetic code tables.
eukaryotic mode. For each name in the list there is a translation_table_NUMBER entry (see
</PARA> below) where NUMBER is its location in the genetic_codes list. Similarly
</SECT2> the start codons are defined as start_codons_NUMBER for each code.
<SECT2 ID="OPTIONS-PROKSTARTCODONS">
<TITLE><LITERAL>prokaryotic_start_codons</LITERAL></TITLE>
<PARA>
This option gives the bases of the possible start codons when &prog; is in
prokaryotic mode.
</PARA> </PARA>
</SECT2> </SECT2>
<SECT2 ID="OPTIONS-TRANSLATION-TABLE"> <SECT2 ID="OPTIONS-TRANSLATION-TABLE">
<TITLE><LITERAL>translation_table</LITERAL></TITLE> <TITLE><LITERAL>translation_table_1</LITERAL></TITLE>
<PARA> <PARA>
The translation_table option is used to lookup codon translations. The 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. table must have exactly 64 entries, and there is one entry for each codon.
...@@ -215,12 +209,12 @@ The entries should appear in this order: ...@@ -215,12 +209,12 @@ The entries should appear in this order:
</SYNOPSIS> </SYNOPSIS>
</PARA> </PARA>
<PARA> <PARA>
This is the default setting for this option: This is the default setting for this option is the Standard Code:
<SYNOPSIS> <SYNOPSIS>
translation_table = \ translation_table_1 = \
f f l l \ f f l l \
s s s s \ s s s s \
y y # + \ y y * * \
c c * w \ c c * w \
\ \
l l l l \ l l l l \
...@@ -239,6 +233,12 @@ translation_table = \ ...@@ -239,6 +233,12 @@ translation_table = \
g g g g g g g g
</SYNOPSIS> </SYNOPSIS>
</PARA> </PARA>
<PARA>
The other translation table entries are defined by giving the differences
to the Standard Code. These are given as the bases that make up the codon
immediately followed by the translation (e.g. atam, so that 'ata' codes
for 'm').
</PARA>
</SECT2> </SECT2>
<SECT2 ID="OPTIONS-EXTRAKEYS"> <SECT2 ID="OPTIONS-EXTRAKEYS">
......
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