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CoreBio

Package corebio :: Module transform :: Class GeneticCode
[frames | no frames]

Type GeneticCode

object --+
         |
        GeneticCode


An encoding of amino acids by DNA triplets.

Example : 

Genetic Code [1]: Standard   
      T         C         A         G      
   +---------+---------+---------+---------+
 T | TTT F   | TCT S   | TAT Y   | TGT C   | T
 T | TTC F   | TCC S   | TAC Y   | TGC C   | C
 T | TTA L   | TCA S   | TAA Stop| TGA Stop| A
 T | TTG L(s)| TCG S   | TAG Stop| TGG W   | G
   +---------+---------+---------+---------+
 C | CTT L   | CCT P   | CAT H   | CGT R   | T
 C | CTC L   | CCC P   | CAC H   | CGC R   | C
 C | CTA L   | CCA P   | CAA Q   | CGA R   | A
 C | CTG L(s)| CCG P   | CAG Q   | CGG R   | G
   +---------+---------+---------+---------+
 A | ATT I   | ACT T   | AAT N   | AGT S   | T
 A | ATC I   | ACC T   | AAC N   | AGC S   | C
 A | ATA I   | ACA T   | AAA K   | AGA R   | A
 A | ATG M(s)| ACG T   | AAG K   | AGG R   | G
   +---------+---------+---------+---------+
 G | GTT V   | GCT A   | GAT D   | GGT G   | T
 G | GTC V   | GCC A   | GAC D   | GGC G   | C
 G | GTA V   | GCA A   | GAA E   | GGA G   | A
 G | GTG V   | GCG A   | GAG E   | GGG G   | G
   +---------+---------+---------+---------+


See Also :
-- http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
-- http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html#7.5
Authors:
    JXG, GEC
Method Summary
  __init__(self, ident, description, amino_acid, start, base1, base2, base3)
Create a new GeneticCode.
  __repr__(self)
  __str__(self)
Returns a text representation of this genetic code.
  back_translate(self, seq)
Convert protein back into coding DNA.
  by_name(name)
Find a genetic code in the code list by name or identifier. (Static method)
  std()
The standard 'universal' genetic code. (Static method)
  std_list()
Return a list of standard genetic codes. (Static method)
  translate(self, seq, frame)
Translate a DNA sequence to a polypeptide using full IUPAC ambiguities in DNA/RNA and amino acid codes.
    Inherited from object
  __delattr__(...)
x.__delattr__('name') <==> del x.name...
  __getattribute__(...)
x.__getattribute__('name') <==> x.name...
  __hash__(x)
x.__hash__() <==> hash(x)...
  __new__(T, S, ...)
T.__new__(S, ...) -> a new object with type S, a subtype of T...
  __reduce__(...)
helper for pickle...
  __reduce_ex__(...)
helper for pickle...
  __setattr__(...)
x.__setattr__('name', value) <==> x.name = value...

Property Summary
  back_table
  table

Instance Method Details

__init__(self, ident, description, amino_acid, start, base1, base2, base3)
(Constructor) 

Create a new GeneticCode.

Args:
-- ident - Standarad identifier (Or zero). An integer
-- description 
-- amino acid - A sequecne of amino acids and stop codons. e.g.
    "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
-- start - A sequence indicating start codons, e.g.,
    "---M---------------M---------------M----------------------------"
-- base1 - The first base of each codon. e.g., 
    "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG"
-- base2 - The second base of each codon. e.g.,
    "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG"
-- base3 - The last base of each codon. e.g., 
    "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG"
Overrides:
__builtin__.object.__init__

__str__(self)
(Informal representation operator) 

Returns a text representation of this genetic code.
Overrides:
__builtin__.object.__str__

back_translate(self, seq) 

Convert protein back into coding DNA.

Args:
-- seq - A polypeptide sequence.

Returns :
-- Seq - A dna sequence

translate(self, seq, frame=0) 

Translate a DNA sequence to a polypeptide using full
IUPAC ambiguities in DNA/RNA and amino acid codes.

Returns : 
-- Seq - A polypeptide sequence

Static Method Details

by_name(name) 

Find a genetic code in the code list by name or identifier.

std() 

The standard 'universal' genetic code.

std_list() 

Return a list of standard genetic codes.

Property Details

back_table

Delete Method:
'A map between amino acids and codons'

table

Delete Method:
'A map between amino acids and codons'

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