biopython

v1.71.0

biopython v1.71.0 Bio.NeuralNetwork.Gene.Schema.SchemaFinder

Find schema in a set of sequences using a genetic algorithm approach.

Finding good schemas is very difficult because it takes forever to enumerate all of the potential schemas. This finder using a genetic algorithm approach to evolve good schema which match many times in a set of sequences.

The default implementation of the finder is ready to find schemas in a set of DNA sequences, but the finder can be customized to deal with any type of data.

Link to this section Summary

Functions

__init__()

Initialize the Schema Finder with its parameters

find()

Find well-represented schemas in the given set of SeqRecords

find_differences()

Find schemas which differentiate between the two sets of SeqRecords

Link to this section Functions

Link to this function __init__()

Initialize the Schema Finder with its parameters.

Arguments:

  • num_schemas — the number of useful (positive fitness) schemas we want to generate.
Link to this function find()

Find well-represented schemas in the given set of SeqRecords.

Link to this function find_differences()

Find schemas which differentiate between the two sets of SeqRecords.