cocoatree.statistics.position.compute_conservation¶

cocoatree.statistics.position.compute_conservation(sequences, seq_weights=None, freq_regul=0.03)[source]¶

Compute the conservation of amino acid at each position.

The conservation is computed as the relative entropy (e.g., the Kullback-Leibler divergence)

\[D_i^a = f_i^a \ln \frac{f_i^a}{q^a} + (1 - f_i^a) \ln \frac{1 - f_i^a}{1 - q^a}\]

where \(f_i^a\) is the observed frequency of amino acid a at: position i`, \(q^a\) is the background expectation

\(D_i^a\) indicates how unlikely the observed frequencies of amino acid a at position i would be if a occurred randomly with probability \(q^a\).

Parameters¶

sequences : list of sequences

seq_weightsndarray (nseq), optional, default: None: if None, will compute sequence weights

freq_regul : regularization parameter (default=__freq_regularization_ref)

Dinp.ndarray (npos,): where each entry corresponds to the conservation at this position in the sequences.