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

# 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 = [
    "flower",
    "blossom",
    "spring",
    "wither",
    "autumn",
    "sunset",
    "ocean",
    "rainbow",
    "clustalx",
    "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()