Package Bio :: Package NeuralNetwork :: Package Gene :: Module Schema
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Module Schema

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Deal with Motifs or Signatures allowing ambiguity in the sequences.

This class contains Schema which deal with Motifs and Signatures at a higher level, by introducing "don't care" (ambiguity) symbols into the sequences. For instance, you could combine the following Motifs:


as all falling under a schema like 'GAT*', where the star indicates a character can be anything. This helps us condense a whole ton of motifs or signatures.

Classes [hide private]
Deal with motifs that have ambiguity characters in it.
Alphabet of a simple Schema for DNA sequences.
Find schemas using a genetic algorithm approach.
Calculate fitness for schemas that differentiate between sequences.
Calculate a fitness giving weight to schemas that match many times.
Generate a random motif within given parameters.
Determine when we are done evolving motifs.
Find schema in a set of sequences using a genetic algorithm approach.
Convert a sequence into a representation of ambiguous motifs (schemas).
Generate Schema from inputs of Motifs or Signatures.
Functions [hide private]
matches_schema(pattern, schema, ambiguity_character='*')
Determine whether or not the given pattern matches the schema.
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Variables [hide private]
  __package__ = 'Bio.NeuralNetwork.Gene'
Function Details [hide private]

matches_schema(pattern, schema, ambiguity_character='*')

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Determine whether or not the given pattern matches the schema.

  • pattern - A string representing the pattern we want to check for matching. This pattern can contain ambiguity characters (which are assumed to be the same as those in the schema).
  • schema - A string schema with ambiguity characters.
  • ambiguity_character - The character used for ambiguity in the schema.