Sequence logo of sequences with equal length

This script creates a sequence logo for the Anderson promoter collection.

# Code source: Patrick Kunzmann
# License: BSD 3 clause

import matplotlib.pyplot as plt
import numpy as np
import biotite.sequence as seq
import biotite.sequence.align as align
import biotite.sequence.graphics as graphics

# The list of Anderson promoters
seqs = [
    seq.NucleotideSequence("ttgacagctagctcagtcctaggtataatgctagc"),
    seq.NucleotideSequence("ttgacagctagctcagtcctaggtataatgctagc"),
    seq.NucleotideSequence("tttacagctagctcagtcctaggtattatgctagc"),
    seq.NucleotideSequence("ttgacagctagctcagtcctaggtactgtgctagc"),
    seq.NucleotideSequence("ctgatagctagctcagtcctagggattatgctagc"),
    seq.NucleotideSequence("ttgacagctagctcagtcctaggtattgtgctagc"),
    seq.NucleotideSequence("tttacggctagctcagtcctaggtactatgctagc"),
    seq.NucleotideSequence("tttacggctagctcagtcctaggtatagtgctagc"),
    seq.NucleotideSequence("tttacggctagctcagccctaggtattatgctagc"),
    seq.NucleotideSequence("ctgacagctagctcagtcctaggtataatgctagc"),
    seq.NucleotideSequence("tttacagctagctcagtcctagggactgtgctagc"),
    seq.NucleotideSequence("tttacggctagctcagtcctaggtacaatgctagc"),
    seq.NucleotideSequence("ttgacggctagctcagtcctaggtatagtgctagc"),
    seq.NucleotideSequence("ctgatagctagctcagtcctagggattatgctagc"),
    seq.NucleotideSequence("ctgatggctagctcagtcctagggattatgctagc"),
    seq.NucleotideSequence("tttatggctagctcagtcctaggtacaatgctagc"),
    seq.NucleotideSequence("tttatagctagctcagcccttggtacaatgctagc"),
    seq.NucleotideSequence("ttgacagctagctcagtcctagggactatgctagc"),
    seq.NucleotideSequence("ttgacagctagctcagtcctagggattgtgctagc"),
    seq.NucleotideSequence("ttgacggctagctcagtcctaggtattgtgctagc"),
]
# Sequences do not need to be aligned
# -> Create alignment with trivial trace
# [[0 0 0 ...]
#  [1 1 1 ...]
#  [2 2 2 ...]
#     ...     ]
alignment = align.Alignment(
    sequences=seqs,
    trace=np.tile(np.arange(len(seqs[0])), len(seqs))
    .reshape(len(seqs), len(seqs[0]))
    .transpose(),
    score=0,
)
# Create sequence logo from alignment
fig = plt.figure(figsize=(8.0, 1.5))
ax = fig.add_subplot(111)
profile = seq.SequenceProfile.from_alignment(alignment)
graphics.plot_sequence_logo(ax, profile, scheme="rainbow")
# Remove the entire frame
ax.axis("off")
fig.tight_layout()
plt.show()