Class ProteinAlignmentAnnotations

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

• aln - alignment.Alignment

Overrides: object.__init__

ruler

A numbering of all the residue indices in an alignment

Get Method:

unreachable.ruler(self) - A numbering of all the residue indices in an alignment

mean_hydrophobicity

returns: A list of floats representing per-column averages of the hydrophobicity of residues in the alignment

Get Method:

unreachable.mean_hydrophobicity(self) - returns: A list of floats representing per-column averages of the hydrophobicity of residues in the alignment

mean_isoelectric_point

returns: A list of floats representing per-column averages of the isoelectric point of residues in the alignment

Get Method:

unreachable.mean_isoelectric_point(self) - returns: A list of floats representing per-column averages of the isoelectric point of residues in the alignment

consensus_symbols

returns: A string including consensus symbols for each alignment position: short_code if unique residue type is most frequent, '+' if there are multiple equally frequent residues in a column, or '.' if there are only gaps in a column.

Get Method:

unreachable.consensus_symbols(self) - returns: A string including consensus symbols for each alignment position: short_code if unique residue type is most frequent, '+' if there are multiple equally frequent residues in a column, or '.' if there are only gaps in a column.

sequence_logo

To create the 'logo' plot, we need frequencies of individual amino acids per alignment position, and overall estimate of column composition diversity ('bits'). This function calculates both measures and returns them as a per-position list of (bits, frequency_dict) tuples.

Get Method:

unreachable.sequence_logo(self) - To create the 'logo' plot, we need frequencies of individual amino acids per alignment position, and overall estimate of column composition diversity ('bits').