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revision 1.5, Wed Apr 22 16:54:56 2015 UTC revision 1.6, Wed Jul 19 23:30:22 2017 UTC
# Line 4  Line 4 
4  #  #
5    
6  #  #
7  # Copyright (c) 2003-2014 University of Chicago and Fellowship  # Copyright (c) 2003-2007 University of Chicago and Fellowship
8  # for Interpretations of Genomes. All Rights Reserved.  # for Interpretations of Genomes. All Rights Reserved.
9  #  #
10  # This file is part of the SEED Toolkit.  # This file is part of the SEED Toolkit.
# Line 24  Line 24 
24    
25  #  #
26  #  Access to the numbered genetic codes used by NCBI.  A code is returned  #  Access to the numbered genetic codes used by NCBI.  A code is returned
27  #  as a reference to a hash that has both uppercase and lowercase translations.  #  as a reference to a hash that has both uppercase and lowercase translations
28    #  of the DNA alphabet.
29  #  #
30  #  There are two access methods: by hash lookup and by function:  #  There are two access methods: by hash lookup and by function:
31  #  #
# Line 40  Line 41 
41  #   \%is_stop_codon = $NCBI_genetic_code::is_stop_codon{ $n };  #   \%is_stop_codon = $NCBI_genetic_code::is_stop_codon{ $n };
42  #   \%is_stop_codon =  NCBI_genetic_code::is_stop_codon( $n );  #   \%is_stop_codon =  NCBI_genetic_code::is_stop_codon( $n );
43  #  #
44  #  The only difference in behaviour is that when no parameter is supplied the  #  The only difference in behaviour is that the subroutine defaults to code
45  #  subroutine defaults to code number 11, but with only the three most common  #  number 1 when no parameter is supplied:
 #  bacterial and archaeal initiator codons:  
46  #  #
47  #   \%genetic_code = NCBI_genetic_code::genetic_code();  #   \%genetic_code_1 =  NCBI_genetic_code::genetic_code();
48  #  #
49  #  All other invalid code numbers return an undefined value.  #  All other invalid numbers return an undefined value.
50  #  #
51    
52  use strict;  use strict;
# Line 106  Line 106 
106      }      }
107  }  }
108    
109  sub genetic_code      { $genetic_code{ $_[0]      || '0' } }  sub genetic_code      { $genetic_code{      $_[0] || '1' } }
110  sub genetic_code_name { $genetic_code_name{ $_[0] || '0' } }  sub genetic_code_name { $genetic_code_name{ $_[0] || '1' } }
111  sub is_start_codon    { $is_start_codon{ $_[0]    || '0' } }  sub is_start_codon    { $is_start_codon{    $_[0] || '1' } }
112  sub is_stop_codon     { $is_stop_codon{ $_[0]     || '0' } }  sub is_stop_codon     { $is_stop_codon{     $_[0] || '1' } }
113    
114  1;  1;
115    
116  __DATA__  __DATA__
117    
 0. The Standard Code with the most common bacterial and archaeal initiators (transl_table=0)  
   
     AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG  
   Starts = ---M-------------------------------M---------------M------------  
   Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG  
   Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG  
   Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG  
   
118  1. The Standard Code (transl_table=1)  1. The Standard Code (transl_table=1)
119    
120      AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG      AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG

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