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

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

.. _sphx_glr_examples_gallery_sequence_homology_hcn_similarity.py:


Dendrogram of a protein family
==============================

This example creates a simple dendrogram for HCN channels and
other proteins of the *cyclic nucleotide–gated* (NCG) ion channel
superfamily.

As distance measure the deviation from sequence identity is used:
For identical sequences the deviation is 0 and for sequences with no
similarity the deviation is 1.
The tree is created using the UPGMA algorithm.

.. GENERATED FROM PYTHON SOURCE LINES 14-94



.. image-sg:: /examples/gallery/sequence/homology/images/sphx_glr_hcn_similarity_001.png
   :alt: Sequence deviation of HCN to other CNG superfamily channels
   :srcset: /examples/gallery/sequence/homology/images/sphx_glr_hcn_similarity_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


    # Code source: Daniel Bauer
    # License: BSD 3 clause

    import matplotlib.pyplot as plt
    import biotite.application.clustalo as clustalo
    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
    import biotite.sequence.phylo as phylo

    UNIPROT_IDS = dict(
        hHCN1="O60741",
        hHCN2="Q9UL51",
        hHCN3="Q9P1Z3",
        hHCN4="Q9Y3Q4",
        spHCN="O76977",
        hEAG1="O95259",
        hERG1="Q12809",
        KAT1="Q39128",
    )


    ### fetch sequences for UniProt IDs from NCBI Entrez
    fasta_file = fasta.FastaFile.read(
        entrez.fetch_single_file(list(UNIPROT_IDS.values()), None, "protein", "fasta")
    )
    sequences = {
        name: seq.ProteinSequence(seq_str)
        for name, seq_str in zip(UNIPROT_IDS.keys(), fasta_file.values())
    }

    ### create a simple phylogenetic tree
    # create MSA
    alignment = clustalo.ClustalOmegaApp.align(list(sequences.values()))
    # build simple tree based on deviation from sequence identity
    distances = 1 - align.get_pairwise_sequence_identity(alignment, mode="shortest")
    tree = phylo.upgma(distances)


    ### plot the tree
    fig, ax = plt.subplots(1, 1, figsize=(8, 5))
    graphics.plot_dendrogram(
        ax,
        tree,
        orientation="left",
        labels=list(UNIPROT_IDS.keys()),
        show_distance=False,
        linewidth=2,
    )
    ax.grid(False)
    ax.set_xticks([])

    # distance indicator
    indicator_len = 0.1
    indicator_start = (
        ax.get_xlim()[0] + ax.get_xlim()[1] * 0.02,
        ax.get_ylim()[1] - ax.get_ylim()[1] * 0.15,
    )
    indicator_stop = (indicator_start[0] + indicator_len, indicator_start[1])
    indicator_center = (
        (indicator_start[0] + indicator_stop[0]) / 2,
        (indicator_start[1] + 0.25),
    )
    ax.annotate(
        "",
        xy=indicator_start,
        xytext=indicator_stop,
        xycoords="data",
        textcoords="data",
        arrowprops={"arrowstyle": "|-|", "linewidth": 2},
    )
    ax.annotate(
        f"{int(indicator_len * 100)} %", xy=indicator_center, ha="center", va="center"
    )
    ax.set_title("Sequence deviation of HCN to other CNG superfamily channels")

    plt.show()


.. _sphx_glr_download_examples_gallery_sequence_homology_hcn_similarity.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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