conkit.plot.sequencecoverage module

A module to produce a sequence coverage plot

class SequenceCoverageFigure(hierarchy, **kwargs)

Bases: conkit.plot.figure.Figure

A Figure object specifically for a Sequence coverage illustration.

This figure will illustrate the coverage of sequences at each position in the provided alignment. It counts the frequency of sequences at which a residue is present and plots it.

This figure can be particularly useful in cases where domain boundaries could be redefined. It is also useful in cases where only parts of your alignment are well covered, and thus trimming the alignment might produce much more accurate Evoluationary Covariance predictions.

hierarchy

The Multiple Sequence Alignment hierarchy

Type:SequenceFile

Examples

>>> import conkit
>>> msa = conkit.io.read('toxd/toxd.a3m', 'a3m')
>>> conkit.plot.SequenceCoverageFigure(msa)

draw()

hierarchy

A ConKit SequenceFile