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Examples¶

This gallery shows examples of possible use cases of Biotite. Some of them are real world examples, others are fictional applications.

Sequences¶

../../_images/sphx_glr_orf_identification_thumb.png

Identification of potential open reading frames¶

../../_images/sphx_glr_operon_map_thumb.png

Feature map of a synthetic operon¶

../../_images/sphx_glr_read_quality_thumb.png

Quality of sequence reads¶

../../_images/sphx_glr_blosum_dendrogram_thumb.png

Dendrogram of the BLOSUM62 matrix¶

../../_images/sphx_glr_luxa_comparison_thumb.png

Sequence comparison of bacterial luciferases¶

../../_images/sphx_glr_avidin_alignment_thumb.png

Pairwise sequence alignment of Avidin with Streptavidin¶

../../_images/sphx_glr_region_visualization_thumb.png

Visualization of region in proximity to lac operon¶

../../_images/sphx_glr_homolog_msa_thumb.png

Multiple sequence alignment of Cas9 homologs¶

../../_images/sphx_glr_color_schemes_thumb.png

Biotite color schemes¶

../../_images/sphx_glr_color_schemes_protein_thumb.png

Biotite color schemes for protein sequences¶

../../_images/sphx_glr_anderson_logo_thumb.png

Sequence logo of the Anderson promoter collection¶

../../_images/sphx_glr_sw_genome_search_thumb.png

Finding homologs of short sequences in a genome¶

../../_images/sphx_glr_lexa_conservation_thumb.png

Conservation of LexA DNA-binding site¶

../../_images/sphx_glr_codon_usage_thumb.png

Calculation of codon usage¶

../../_images/sphx_glr_pi3k_alignment_thumb.png

Comparison of human PI3K family¶

../../_images/sphx_glr_hcn_hydropathy_thumb.png

Hydropathy and conservation of HCN channels¶

Structures¶

../../_images/sphx_glr_diameter_thumb.png

Calculation of protein diameter¶

../../_images/sphx_glr_adjacency_matrix_thumb.png

Construction of an adjacency matrix¶

../../_images/sphx_glr_ramachandran_thumb.png

Ramachandran plot of dynein motor domain¶

../../_images/sphx_glr_domain_hbonds_thumb.png

Hydrogen bonds between protein domains¶

../../_images/sphx_glr_mmtf_trajectory_thumb.png

MMTF as trajectory format¶

../../_images/sphx_glr_ku_superimposition_thumb.png

Superimposition of two protein structures¶

../../_images/sphx_glr_residue_chirality_thumb.png

Determination of amino acid enantiomers¶

../../_images/sphx_glr_mmtf_archive_noexec_thumb.png

Creating an MMTF based PDB archive¶

../../_images/sphx_glr_solvation_shells_thumb.png

Solvation shells of sodium and chloride ions¶

../../_images/sphx_glr_gap_bars_thumb.png

Missing residues in protein structures of DNA-PKcs¶

../../_images/sphx_glr_md_analysis_thumb.png

Basic analysis of MD simulation¶

../../_images/sphx_glr_pb_alignment_thumb.png

Structural alignment of lysozyme variants using ‘Protein Blocks’¶

../../_images/sphx_glr_transketolase_sse_thumb.png

Four ways to get the secondary structure of a protein¶

Download all examples in Python source code: gallery_python.zip

Download all examples in Jupyter notebooks: gallery_jupyter.zip

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