Skip to main content
Ctrl+K
Biotite - Home
  • Tutorial
  • Installation
  • API Reference
  • Examples
  • Extensions
  • Contributor guide
  • Logo
  • GitHub
  • PyPI
  • News
  • Tutorial
  • Installation
  • API Reference
  • Examples
  • Extensions
  • Contributor guide
  • Logo
  • GitHub
  • PyPI
  • News

Section Navigation

  • Sequence examples
    • Homology and alignment
      • Pairwise sequence alignment of protein sequences
      • Customized visualization of a multiple sequence alignment
      • Finding homologous regions in two genomes
      • Finding homologs of a gene in a genome
      • Phylogenetic tree of a protein family
      • Hydropathy and conservation of ion channels
      • Dendrogram of a protein family
      • Homology search and multiple sequence alignment
      • Conservation of binding site
      • Fetching and aligning a protein from different species
      • Display sequence similarity in a heat map
      • Plot epitope mapping data onto protein sequence alignments
      • Mutual information as measure for coevolution of residues
      • Polymorphisms in a gene
    • Sequence read quality control and mapping
      • Quantifying gene expression from RNA-seq data
      • Comparative genome assembly
      • Quality control of sequencing data
      • Quality of sequence reads
    • Sequence profiles
      • Sequence logo of sequences with equal length
      • Identification of a binding site by sequence conservation
    • Features and annotations
      • Feature map of a synthetic operon
      • Plasmid map of a vector
      • Visualization of a custom plasmid
      • Visualization of a region in proximity to a feature
      • Domains of bacterial sigma factors
    • Miscellaneous
      • Dendrogram of a substitution matrix
      • Calculation of codon usage
      • Biotite color schemes
      • Biotite color schemes for protein sequences
      • Statistics of local alignments and the E-value
      • Identification of potential open reading frames
  • Structure examples
    • Protein backbone and secondary structure
      • Assembly of a straight peptide from sequence
      • Ramachandran plot of dynein motor domain
      • Determination of amino acid enantiomers
      • Arrangement of beta-sheets
      • Three ways to get the secondary structure of a protein
    • Nucleic acid base pairs and secondary structure
      • Plotting the base pairs of a tRNA-like-structure
      • Leontis-Westhof Nomenclature
      • Comparison of a tRNA-like-structure with a tRNA
      • Visualization of Watson-Crick base pairs
    • Small molecules
      • Enumeration of alkane isomers
      • Molecular visualization of a small molecule using Matplotlib
      • Partial charge distribution
    • Proximity and contacts
      • Construction of an adjacency matrix
      • Contact sites of protein-DNA interaction
      • Detection of disulfide bonds
      • Hydrogen bonds between protein domains
      • Identification of lipid bilayer leaflets
    • Molecular dynamics and docking
      • Docking a ligand to a receptor
      • Basic analysis of a MD simulation
      • BinaryCIF as trajectory format
      • LDDT for predicted structure evaluation
      • Visualization of normal modes from an elastic network model
      • Creation of an amino acid rotamer library
      • Analysis of solvation shells
      • Secondary structure during an MD simulation
      • Cavity solvation in different states of an ion channel
    • Structural alphabets
      • Multiple Structural alignment of orthologous proteins
      • Searching for structural homologs in a protein structure database
    • Miscellaneous
      • Biological assembly of a structure
      • Calculation of protein diameter
      • Identifying unresolved regions in protein structures
      • Visualization of glycosylated amino acids
      • Superimposition of homologous protein structures
      • Annual releases of PDB structures
  • Examples
  • Sequence examples
  • Miscellaneous

Miscellaneous#

Dendrogram of a substitution matrix

Dendrogram of a substitution matrix

Calculation of codon usage

Calculation of codon usage

Biotite color schemes

Biotite color schemes

Biotite color schemes for protein sequences

Biotite color schemes for protein sequences

Statistics of local alignments and the E-value

Statistics of local alignments and the E-value

Identification of potential open reading frames

Identification of potential open reading frames
Edit on GitHub
Show Source

© Copyright The Biotite contributors.

Created using Sphinx 8.2.3.

Built with the PyData Sphinx Theme 0.15.4.