Information analysis of an alignment

Information here is in the formal sense – maximum entropy minus the entropy at a position. This is fast to compute and is an indicator of the variability at a position.

Illustrated with a simple example

from cogent3 import make_seq, make_aligned_seqs, load_aligned_seqs

s1 = make_seq('TGATGTAAGGTAGTT', name='s1', moltype="dna")
s2 = make_seq('--CTGGAAGGGT---', name='s2', moltype="dna")

seqs = make_aligned_seqs(data=[s1, s2], array_align=False,
                         moltype='dna')
draw = seqs.information_plot(window=2, include_gap=True)
draw.show(width=500, height=400)

On a sample data set

Clicking on any of the legend items causes that to disappear from the plot.

aln = load_aligned_seqs('../data/brca1.fasta', moltype='protein')

fig = aln.information_plot(stat='median')
fig.show(width=500, height=400)