biopython

v1.71.0

biopython v1.71.0 Bio.NeuralNetwork.Gene.Motif.MotifCoder

Convert motifs and a sequence into neural network representations.

This is designed to convert a sequence into a representation that can be fed as an input into a neural network. It does this by representing a sequence based the motifs present.

Link to this section Summary

Functions

__init__()

Initialize an input producer with motifs to look for

representation()

Represent a sequence as a set of motifs

Link to this section Functions

Link to this function __init__()

Initialize an input producer with motifs to look for.

Arguments:

  • motifs - A complete list of motifs, in order, that are to be searched for in a sequence.
Link to this function representation()

Represent a sequence as a set of motifs.

Arguments:

  • sequence - A Bio.Seq object to represent as a motif.

This converts a sequence into a representation based on the motifs. The representation is returned as a list of the relative amount of each motif (number of times a motif occurred divided by the total number of motifs in the sequence). The values in the list correspond to the input order of the motifs specified in the initializer.