transdecode.TranssysDNADecoder

Class TranssysDNADecoder

Decodes genome sequences into transsys programs. The overall gene structure is:

...|----activator area-----|----repressor area ----|-geneStart-|--structural area--|-geneEnd... |<-activatorAreaLength->|<-repressorAreaLength->|

The structural area length is variable. Gene start and end can also be variable, as enabled by regular expressions.

This decoder uses the following constants:

geneStartRE, geneEndRE: Regular expressions to determine start and end of a gene

repressorAreaLength: length of area where binding represses

activationAreaLength: length of area where binding activates

decay, diffusibility: constants for factor construction

a_spec, a_max: constants for promoter element construction (used for both activate and repress elements)

constitutive: constant for constitutive promoter element construction

Notice that strength of activation / repression does not depend on binding strength in this decoder.

Instance Methods

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__init__(self)

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__str__(self)

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write(self, f)

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parse(self, f)

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setGeneStartRE(self, r)

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setGeneEndRE(self, r)

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rawDNAGenes(self, genome)
separate a genome into raw genes.

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decode_transsys(self, transsys_name, genome)
construct a transsys program by decoding a genome sequence.

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Class Variables

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savefile_magic = 'TranssysDNADecoderParameters-1.3'

decode_transsys(self, transsys_name, genome)

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construct a transsys program by decoding a genome sequence. The process is: (1) split the genome into sequence portions that represent genes, based on the gene start and end regular expressions. (2) For each Gene, translate the structural parts of a gene into a DNABinder; the set of all DNABinders constitutes the proteome. (3) For each gene, determine the multiset of DNABinders that bind in the activating and the repressing regions, respectively. (4) Construct a transsys program of the genes and the proteome found, with promoters constructed based on (3).