biopython v1.71.0 Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness
Calculate fitness for schemas that differentiate between sequences.
Link to this section Summary
Link to this section Functions
Link to this function
__init__()
Initialize with different sequences to evaluate.
Arguments:
- positive_seq - A list of SeqRecord objects which are the ‘positive’ sequences — the ones we want to select for.
- negative_seq - A list of SeqRecord objects which are the ‘negative’ sequences that we want to avoid selecting.
- schema_evaluator - An Schema class which can be used to evaluate find motif matches in sequences.
Link to this function
calculate_fitness()
Calculate the fitness for a given schema.
Fitness is specified by the number of occurrences of the schema in the positive sequences minus the number of occurrences in the negative examples.
This fitness is then modified by multiplying by the length of the schema and then dividing by the number of ambiguous characters in the schema. This helps select for schema which are longer and have less redundancy.