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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:
'GATC', 'GATG', 'GATG', 'GATT'
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.
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Schema Deal with motifs that have ambiguity characters in it. |
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SchemaDNAAlphabet Alphabet of a simple Schema for DNA sequences. |
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GeneticAlgorithmFinder Find schemas using a genetic algorithm approach. |
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DifferentialSchemaFitness Calculate fitness for schemas that differentiate between sequences. |
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MostCountSchemaFitness Calculate a fitness giving weight to schemas that match many times. |
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RandomMotifGenerator Generate a random motif within given parameters. |
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SimpleFinisher Determine when we are done evolving motifs. |
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SchemaFinder Find schema in a set of sequences using a genetic algorithm approach. |
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SchemaCoder Convert a sequence into a representation of ambiguous motifs (schemas). |
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SchemaFactory Generate Schema from inputs of Motifs or Signatures. |
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__package__ =
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Determine whether or not the given pattern matches the schema. Arguments: o 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). o schema - A string schema with ambiguity characters. o ambiguity_character - The character used for ambiguity in the schema. |
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