.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/gallery/sequence/avidin_alignment.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_avidin_alignment.py>`
        to download the full example code

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

.. _sphx_glr_examples_gallery_sequence_avidin_alignment.py:


Pairwise sequence alignment of Avidin with Streptavidin
=======================================================

This script performs a pairwise sequence alignment of
avidin (*Gallus gallus*)
with streptavidin (*Streptomyces lavendulae*).

.. GENERATED FROM PYTHON SOURCE LINES 9-48



.. image-sg:: /examples/gallery/sequence/images/sphx_glr_avidin_alignment_001.png
   :alt: avidin alignment
   :srcset: /examples/gallery/sequence/images/sphx_glr_avidin_alignment_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


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

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

    # Download and parse protein sequences of avidin and streptavidin
    fasta_file = fasta.FastaFile.read(entrez.fetch_single_file(
        ["CAC34569", "ACL82594"], None, "protein", "fasta"
    ))
    for name, sequence in fasta_file.items():
        if "CAC34569" in name:
            avidin_seq = seq.ProteinSequence(sequence)
        elif "ACL82594" in name:
            streptavidin_seq = seq.ProteinSequence(sequence)

    # Get BLOSUM62 matrix
    matrix = align.SubstitutionMatrix.std_protein_matrix()
    # Perform pairwise sequence alignment with affine gap penalty
    # Terminal gaps are not penalized
    alignments = align.align_optimal(avidin_seq, streptavidin_seq, matrix,
                                     gap_penalty=(-10, -1), terminal_penalty=False)

    # Draw first and only alignment
    # The color intensity indicates the similiarity
    fig = plt.figure(figsize=(8.0, 2.5))
    ax = fig.add_subplot(111)
    graphics.plot_alignment_similarity_based(
        ax, alignments[0], matrix=matrix, labels=["Avidin", "Streptavidin"],
        show_numbers=True, show_line_position=True
    )
    fig.tight_layout()

    plt.show()


.. _sphx_glr_download_examples_gallery_sequence_avidin_alignment.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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