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

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

.. _sphx_glr_examples_gallery_sequence_profile_anderson_logo.py:


Sequence logo of sequences with equal length
============================================

This script creates a sequence logo for the
`Anderson promoter collection <http://parts.igem.org/Promoters/Catalog/Anderson>`_.

.. GENERATED FROM PYTHON SOURCE LINES 8-63



.. image-sg:: /examples/gallery/sequence/profile/images/sphx_glr_anderson_logo_001.png
   :alt: anderson logo
   :srcset: /examples/gallery/sequence/profile/images/sphx_glr_anderson_logo_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


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

    import matplotlib.pyplot as plt
    import numpy as np
    import biotite.sequence as seq
    import biotite.sequence.align as align
    import biotite.sequence.graphics as graphics

    # The list of Anderson promoters
    seqs = [
        seq.NucleotideSequence("ttgacagctagctcagtcctaggtataatgctagc"),
        seq.NucleotideSequence("ttgacagctagctcagtcctaggtataatgctagc"),
        seq.NucleotideSequence("tttacagctagctcagtcctaggtattatgctagc"),
        seq.NucleotideSequence("ttgacagctagctcagtcctaggtactgtgctagc"),
        seq.NucleotideSequence("ctgatagctagctcagtcctagggattatgctagc"),
        seq.NucleotideSequence("ttgacagctagctcagtcctaggtattgtgctagc"),
        seq.NucleotideSequence("tttacggctagctcagtcctaggtactatgctagc"),
        seq.NucleotideSequence("tttacggctagctcagtcctaggtatagtgctagc"),
        seq.NucleotideSequence("tttacggctagctcagccctaggtattatgctagc"),
        seq.NucleotideSequence("ctgacagctagctcagtcctaggtataatgctagc"),
        seq.NucleotideSequence("tttacagctagctcagtcctagggactgtgctagc"),
        seq.NucleotideSequence("tttacggctagctcagtcctaggtacaatgctagc"),
        seq.NucleotideSequence("ttgacggctagctcagtcctaggtatagtgctagc"),
        seq.NucleotideSequence("ctgatagctagctcagtcctagggattatgctagc"),
        seq.NucleotideSequence("ctgatggctagctcagtcctagggattatgctagc"),
        seq.NucleotideSequence("tttatggctagctcagtcctaggtacaatgctagc"),
        seq.NucleotideSequence("tttatagctagctcagcccttggtacaatgctagc"),
        seq.NucleotideSequence("ttgacagctagctcagtcctagggactatgctagc"),
        seq.NucleotideSequence("ttgacagctagctcagtcctagggattgtgctagc"),
        seq.NucleotideSequence("ttgacggctagctcagtcctaggtattgtgctagc"),
    ]
    # Sequences do not need to be aligned
    # -> Create alignment with trivial trace
    # [[0 0 0 ...]
    #  [1 1 1 ...]
    #  [2 2 2 ...]
    #     ...     ]
    alignment = align.Alignment(
        sequences=seqs,
        trace=np.tile(np.arange(len(seqs[0])), len(seqs))
        .reshape(len(seqs), len(seqs[0]))
        .transpose(),
        score=0,
    )
    # Create sequence logo from alignment
    fig = plt.figure(figsize=(8.0, 1.5))
    ax = fig.add_subplot(111)
    profile = seq.SequenceProfile.from_alignment(alignment)
    graphics.plot_sequence_logo(ax, profile, scheme="rainbow")
    # Remove the entire frame
    ax.axis("off")
    fig.tight_layout()
    plt.show()


.. _sphx_glr_download_examples_gallery_sequence_profile_anderson_logo.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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