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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:
Notice that strength of activation / repression does not depend on binding strength in this decoder.
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savefile_magic = 'TranssysDNADecoderParameters-1.3'
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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). |
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