.. _sphx_glr_examples_gallery_sequence_homology:

Homology and alignment
----------------------


.. raw:: html

    <div class="sphx-glr-thumbnails">


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    <div class="sphx-glr-thumbcontainer" tooltip="This script performs a pairwise sequence alignment of avidin (Gallus gallus) with streptavidin ...">

.. only:: html

  .. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_avidin_alignment_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_sequence_homology_avidin_alignment.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Pairwise sequence alignment of protein sequences</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows an alignment visualization used by the serious game Bionigma Hess2014. This ...">

.. only:: html

  .. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_bionigma_alignment_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_sequence_homology_bionigma_alignment.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Customized visualization of a multiple sequence alignment</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Presumably, plant cells obtained its ability for photosynthesis through endosymbiosis: In the p...">

.. only:: html

  .. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_genome_comparison_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_sequence_homology_genome_comparison.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Finding homologous regions in two genomes</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this example we use a combination of a KmerTable and align_banded() to search a genome for h...">

.. only:: html

  .. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_genome_search_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_sequence_homology_genome_search.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Finding homologs of a gene in a genome</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example plots an unrooted phylogenetic tree depicting the evolution of different G-protein...">

.. only:: html

  .. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_gpcr_evolution_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_sequence_homology_gpcr_evolution.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Phylogenetic tree of a protein family</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This script creates a hydropathy plot of the human HCN1 channel protein and compares it with th...">

.. only:: html

  .. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_hcn_hydropathy_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_sequence_homology_hcn_hydropathy.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Hydropathy and conservation of ion channels</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example creates a simple dendrogram for HCN channels and other proteins of the cyclic nucl...">

.. only:: html

  .. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_hcn_similarity_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_sequence_homology_hcn_similarity.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Dendrogram of a protein family</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This script searches for proteins homologous to Cas9 from Streptococcus pyogenes via NCBI BLAST...">

.. only:: html

  .. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_homolog_msa_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_sequence_homology_homolog_msa.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Homology search and multiple sequence alignment</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The web page on sequence logos on Wikipedia shows the sequence logo of the LexA-binding motif o...">

.. only:: html

  .. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_lexa_conservation_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_sequence_homology_lexa_conservation.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Conservation of binding site</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This script creates a multiple sequence alignment of the bacterial luciferase gene luxA using t...">

.. only:: html

  .. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_luxa_comparison_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_sequence_homology_luxa_comparison.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Fetching and aligning a protein from different species</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The following script visualizes the sequence alignment of six proteins of the human Phosphoinos...">

.. only:: html

  .. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_pi3k_alignment_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_sequence_homology_pi3k_alignment.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Display sequence similarity in a heat map</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Peptide arrays can be used as a high-throughput platform for screening biological interactions....">

.. only:: html

  .. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_plotepiscan_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_sequence_homology_plotepiscan.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Plot epitope mapping data onto protein sequence alignments</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Mutual information (MI) is a broadly used measure for the coevolution between two residues of a...">

.. only:: html

  .. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_residue_coevolution_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_sequence_homology_residue_coevolution.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Mutual information as measure for coevolution of residues</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The THCA synthase catalyzes the last step in the synthesis of tetrahydrocannabinolic acid (THCA...">

.. only:: html

  .. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_thca_synthase_polymorphism_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_sequence_homology_thca_synthase_polymorphism.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Polymorphisms in a gene</div>
    </div>


.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/gallery/sequence/homology/avidin_alignment
   /examples/gallery/sequence/homology/bionigma_alignment
   /examples/gallery/sequence/homology/genome_comparison
   /examples/gallery/sequence/homology/genome_search
   /examples/gallery/sequence/homology/gpcr_evolution
   /examples/gallery/sequence/homology/hcn_hydropathy
   /examples/gallery/sequence/homology/hcn_similarity
   /examples/gallery/sequence/homology/homolog_msa
   /examples/gallery/sequence/homology/lexa_conservation
   /examples/gallery/sequence/homology/luxa_comparison
   /examples/gallery/sequence/homology/pi3k_alignment
   /examples/gallery/sequence/homology/plotepiscan
   /examples/gallery/sequence/homology/residue_coevolution
   /examples/gallery/sequence/homology/thca_synthase_polymorphism