Package Bio :: Package MEME :: Module Motif :: Class MEMEMotif
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Class MEMEMotif

Motif --+
        |
       MEMEMotif


A subclass of Motif used in parsing MEME (and MAST) output.

This sublcass defines functions and data specific to MEME motifs. This includes the evalue for a motif and the PSSM of the motif.

Methods: add_instance_from_values (name = 'default', pvalue = 1, sequence = 'ATA', start = 0, strand = +): create a new instance of the motif with the specified values. add_to_pssm (position): add a new position to the pssm. The position should be a list of nucleotide/amino acid frequencies add_to_logodds (position): add a new position to the log odds matrix. The position should be a tuple of log odds values for the nucleotide/amino acid at that position. compare_motifs (other_motif): returns the maximum correlation between this motif and other_motif
Method Summary
  __init__(self)
  add_instance_from_values(self, name, pvalue, sequence, start, strand)
  add_to_logodds(self, thisposition)
  add_to_pssm(self, thisposition)
  compare_motifs(self, motif)
    Inherited from Motif
  add_instance(self, instance)
  get_instance_by_name(self, name)
  make_consensus(self, minimum_frequency)
  make_pssm(self)

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