Logo

A comprehensive library for computational molecular biology

Navigation

  • Install instructions
  • Tutorial
  • API Reference
  • Examples
  • Extensions
  • Development guide
  • Biotite logo

Quick search


GitHub PyPI Twitter

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_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_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¶

Download all examples in Python source code: gallery_python.zip

Download all examples in Jupyter notebooks: gallery_jupyter.zip

Gallery generated by Sphinx-Gallery

©2017-2018, the Biotite contributors. | Powered by Sphinx 2.0.1 & Alabaster 0.7.12 | Page source
Fork me on GitHub