Class ProteinAlignmentAnnotations

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

Parameters:

• aln - alignment.Alignment

Overrides: object.__init__

indices

A numbering of all the column indices in an alignment

Get Method:

unreachable.indices(self) - A numbering of all the column 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_seq

Consensus sequence in the alignment. If there is more than one highest freq. residue in the column, save all of them.

Get Method:

unreachable.consensus_seq(self) - Consensus sequence in the alignment.

Type:

list of list of 1-letter strings

consensus_freq

Frequencies of the consensus residue in each alignment column Gapped positions are counted when calculating frequencies.

Get Method:

unreachable.consensus_freq(self) - Frequencies of the consensus residue in each alignment column Gapped positions are counted when calculating frequencies.

consensus_symbols

Consensus symbols in the alignment based on pre-defined residue sets, same as in ClustalW

Get Method:

unreachable.consensus_symbols(self) - Consensus symbols in the alignment based on pre-defined residue sets, same as in ClustalW

Type:

A list of ConsensusSymbol enums.

sequence_logo

Calculates frequencies of individual amino acids per alignment position, and overall estimate of column composition diversity ('bits').

Schneider TD, Stephens RM (1990). "Sequence Logos: A New Way to Display Consensus Sequences". Nucleic Acids Res 18 (20): 6097–6100. doi:10.1093/nar/18.20.6097

Get Method:

unreachable.sequence_logo(self) - Calculates frequencies of individual amino acids per alignment position, and overall estimate of column composition diversity ('bits').

Type:

list of tuples, each tuple consists of a float (bits), and a list of tuples (<short_code>, freq) in the increasing order of frequency.