Biotite color schemes for protein sequences

This script shows the same multiple protein sequence alignment in the different color schemes available in Biotite.

• rainbow - Default color scheme in Biotite

• clustalx - Default color scheme of the ClustalX software

• Color schemes generated with the software Gecos 1:

  • flower - Light color scheme, based on BLOSUM62

  • blossom - Light color scheme with high contrast, based on BLOSUM62, depicts symbol similarity worse than flower

  • spring - Light color scheme, based on BLOSUM62, with alanine fixed to gray

  • wither - Dark color scheme, analogous to blossom

  • autumn - Dark color scheme, analogous to spring

  • sunset - Red-green color vision deficiency adapated color scheme, based on BLOSUM62

  • ocean - Blue shifted, light color scheme, based on BLOSUM62

• Color schemes adapted from JalView 2:

  • zappo - Color scheme that depicts physicochemical properties

  • taylor - Color scheme invented by Willie Taylor

  • buried - Color scheme depicting the buried index

  • hydrophobicity - Color scheme depicting hydrophobicity

  • prophelix - Color scheme depicting secondary structure propensities

  • propstrand - Color scheme depicting secondary structure propensities

  • propturn - Color scheme depicting secondary structure propensities

1

P. Kunzmann, B. E. Mayer, K. Hamacher, “Substitution matrix based color schemes for sequence alignment visualization,” BMC Bioinformatics, vol. 21, pp. 209, May 2020. doi: 10.1186/s12859-020-3526-6

2

M. Clamp, J. Cuff, S. M. Searle, G. J. Barton, “The Jalview Java alignment editor,” Bioinformatics, vol. 20, pp. 426–427, February 2004. doi: 10.1093/bioinformatics/btg430

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

import numpy as np
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
import biotite.sequence as seq
import biotite.sequence.io.fasta as fasta
import biotite.sequence.align as align
import biotite.sequence.graphics as graphics
import biotite.database.entrez as entrez


# Generate example alignment
# (the same as in the bacterial luciferase example)
query =   entrez.SimpleQuery("luxA", "Gene Name") \
        & entrez.SimpleQuery("srcdb_swiss-prot", "Properties")
uids = entrez.search(query, db_name="protein")
fasta_file = fasta.FastaFile.read(entrez.fetch_single_file(
    uids, None, db_name="protein", ret_type="fasta"
))
sequences = [seq.ProteinSequence(seq_str) for seq_str in fasta_file.values()]
matrix = align.SubstitutionMatrix.std_protein_matrix()
alignment, order, _, _ = align.align_multiple(sequences, matrix)
# Order alignment according to the guide tree
alignment = alignment[:, order]
alignment = alignment[220:300]

# Get color scheme names
alphabet = seq.ProteinSequence.alphabet
schemes = [
    "rainbow", "clustalx",
    "flower", "blossom", "spring", "wither", "autumn", "sunset", "ocean",
    "zappo", "taylor", "buried", "hydrophobicity",
    "prophelix", "propstrand", "propturn"
]
count = len(schemes)
# Assert that this example displays all available amino acid color schemes
all_schemes = graphics.list_color_scheme_names(alphabet)
assert set(schemes) == set(all_schemes)


# Visualize each scheme using the example alignment
fig = plt.figure(figsize=(8.0, count*2.0))
gridspec = GridSpec(2, count)
for i, name in enumerate(schemes):
    for j, color_symbols in enumerate([False, True]):
        ax = fig.add_subplot(count, 2, 2*i + j + 1)
        if j == 0:
            ax.set_ylabel(name)
            alignment_part = alignment[:40]
        else:
            alignment_part = alignment[40:]
        graphics.plot_alignment_type_based(
            ax, alignment_part, symbols_per_line=len(alignment_part),
            color_scheme=name, color_symbols=color_symbols, symbol_size=8
        )
fig.tight_layout()
fig.subplots_adjust(wspace=0)
plt.show()