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Sequence examples
=================
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Homology and alignment
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.. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_avidin_alignment_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_homology_avidin_alignment.py`
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Pairwise sequence alignment of protein sequences
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.. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_bionigma_alignment_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_homology_bionigma_alignment.py`
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Customized visualization of a multiple sequence alignment
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.. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_genome_comparison_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_homology_genome_comparison.py`
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Finding homologous regions in two genomes
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.. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_genome_search_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_homology_genome_search.py`
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Finding homologs of a gene in a genome
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.. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_gpcr_evolution_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_homology_gpcr_evolution.py`
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Phylogenetic tree of a protein family
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.. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_hcn_hydropathy_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_homology_hcn_hydropathy.py`
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Hydropathy and conservation of ion channels
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.. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_hcn_similarity_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_homology_hcn_similarity.py`
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Dendrogram of a protein family
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.. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_homolog_msa_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_homology_homolog_msa.py`
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Homology search and multiple sequence alignment
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.. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_lexa_conservation_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_homology_lexa_conservation.py`
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Conservation of binding site
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.. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_luxa_comparison_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_homology_luxa_comparison.py`
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Fetching and aligning a protein from different species
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.. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_pi3k_alignment_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_homology_pi3k_alignment.py`
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Display sequence similarity in a heat map
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.. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_plotepiscan_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_homology_plotepiscan.py`
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Plot epitope mapping data onto protein sequence alignments
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.. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_residue_coevolution_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_homology_residue_coevolution.py`
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Mutual information as measure for coevolution of residues
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.. image:: /examples/gallery/sequence/homology/images/thumb/sphx_glr_thca_synthase_polymorphism_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_homology_thca_synthase_polymorphism.py`
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Polymorphisms in a gene
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Sequence read quality control and mapping
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.. image:: /examples/gallery/sequence/sequencing/images/thumb/sphx_glr_gene_counts_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_sequencing_gene_counts.py`
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Quantifying gene expression from RNA-seq data
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.. image:: /examples/gallery/sequence/sequencing/images/thumb/sphx_glr_genome_assembly_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_sequencing_genome_assembly.py`
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Comparative genome assembly
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.. image:: /examples/gallery/sequence/sequencing/images/thumb/sphx_glr_quality_control_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_sequencing_quality_control.py`
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Quality control of sequencing data
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.. image:: /examples/gallery/sequence/sequencing/images/thumb/sphx_glr_read_quality_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_sequencing_read_quality.py`
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Quality of sequence reads
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Sequence profiles
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.. image:: /examples/gallery/sequence/profile/images/thumb/sphx_glr_anderson_logo_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_profile_anderson_logo.py`
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Sequence logo of sequences with equal length
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.. image:: /examples/gallery/sequence/profile/images/thumb/sphx_glr_rbs_identification_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_profile_rbs_identification.py`
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Identification of a binding site by sequence conservation
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Features and annotations
------------------------
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.. image:: /examples/gallery/sequence/annotation/images/thumb/sphx_glr_operon_map_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_annotation_operon_map.py`
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Feature map of a synthetic operon
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.. image:: /examples/gallery/sequence/annotation/images/thumb/sphx_glr_plasmid_map_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_annotation_plasmid_map.py`
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Plasmid map of a vector
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.. image:: /examples/gallery/sequence/annotation/images/thumb/sphx_glr_plasmid_map_custom_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_annotation_plasmid_map_custom.py`
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Visualization of a custom plasmid
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.. image:: /examples/gallery/sequence/annotation/images/thumb/sphx_glr_region_visualization_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_annotation_region_visualization.py`
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Visualization of a region in proximity to a feature
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.. image:: /examples/gallery/sequence/annotation/images/thumb/sphx_glr_sigma_domains_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_annotation_sigma_domains.py`
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Domains of bacterial sigma factors
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Miscellaneous
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.. image:: /examples/gallery/sequence/misc/images/thumb/sphx_glr_blosum_dendrogram_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_misc_blosum_dendrogram.py`
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Dendrogram of a substitution matrix
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.. image:: /examples/gallery/sequence/misc/images/thumb/sphx_glr_codon_usage_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_misc_codon_usage.py`
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Calculation of codon usage
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.. image:: /examples/gallery/sequence/misc/images/thumb/sphx_glr_color_schemes_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_misc_color_schemes.py`
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Biotite color schemes
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.. image:: /examples/gallery/sequence/misc/images/thumb/sphx_glr_color_schemes_protein_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_misc_color_schemes_protein.py`
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Biotite color schemes for protein sequences
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.. image:: /examples/gallery/sequence/misc/images/thumb/sphx_glr_local_alignment_statistics_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_misc_local_alignment_statistics.py`
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Statistics of local alignments and the E-value
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.. image:: /examples/gallery/sequence/misc/images/thumb/sphx_glr_orf_identification_thumb.png
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:ref:`sphx_glr_examples_gallery_sequence_misc_orf_identification.py`
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Identification of potential open reading frames
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.. toctree::
:hidden:
:includehidden:
/examples/gallery/sequence/homology/index.rst
/examples/gallery/sequence/sequencing/index.rst
/examples/gallery/sequence/profile/index.rst
/examples/gallery/sequence/annotation/index.rst
/examples/gallery/sequence/misc/index.rst
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.. rst-class:: sphx-glr-signature
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