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_color_schemes_thumb.png

Biotite color schemes

../../_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_anderson_logo_thumb.png

Sequence logo of the Anderson promoter collection

../../_images/sphx_glr_lexa_conservation_thumb.png

Conservation of LexA DNA-binding site

../../_images/sphx_glr_sw_genome_search_thumb.png

Finding homologs of short sequences in a genome

../../_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_transketolase_sse_thumb.png

Four ways to get the secondary structure of a protein

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