Module transdecode :: Class DNABinder
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Class DNABinder

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Represents a DNA binding factor using a scoring matrix and a threshold.

Instance Methods [hide private]
 
__init__(self, name, dna, thresholdBase, thresholdIncrement) source code
 
decode(self, dna, thresholdBase, thresholdIncrement)
Decode a string of dna bases to a matrix and a threshold.
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__str__(self) source code
 
max_score(self) source code
 
bindingEnergy(self, seq) source code
 
bindingSite(self, seq, position=0) source code
Method Details [hide private]

decode(self, dna, thresholdBase, thresholdIncrement)

source code 

Decode a string of dna bases to a matrix and a threshold. The matrix is decoded by taking words of length 5 from the encoding sequence. If the first four characters are all identical, decoding stops. Otherwise, they are mapped to integer values in {0, 1, 2, 3} and appended to the matrix as a further column. The 5th character is mapped to an integer, which is and added to the threshold. The threshold is further controlled by the threshold offset, which is also added to the threshold for each position in the matrix, thus allowing some control over the binder's specificity.