.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/gallery/sequence/misc/color_schemes_protein.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_examples_gallery_sequence_misc_color_schemes_protein.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_examples_gallery_sequence_misc_color_schemes_protein.py:


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*
      :footcite:`Kunzmann2020`:

      - **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* :footcite:`Clamp2004`:

      - **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

.. footbibliography::

.. GENERATED FROM PYTHON SOURCE LINES 41-117



.. image-sg:: /examples/gallery/sequence/misc/images/sphx_glr_color_schemes_protein_001.png
   :alt: color schemes protein
   :srcset: /examples/gallery/sequence/misc/images/sphx_glr_color_schemes_protein_001.png, /examples/gallery/sequence/misc/images/sphx_glr_color_schemes_protein_001_2_00x.png 2.00x
   :class: sphx-glr-single-img





.. code-block:: Python


    # 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()


.. _sphx_glr_download_examples_gallery_sequence_misc_color_schemes_protein.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: color_schemes_protein.ipynb <color_schemes_protein.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: color_schemes_protein.py <color_schemes_protein.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: color_schemes_protein.zip <color_schemes_protein.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_