Information analysis of an alignment

Note

These docs now use the new_type core objects via the following setting.

import os

# using new types without requiring an explicit argument
os.environ["COGENT3_NEW_TYPE"] = "1"

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 load_aligned_seqs, make_aligned_seqs, make_seq

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)