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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
  • Sequence profiles

Sequence profiles#

Sequence logo of sequences with equal length

Sequence logo of sequences with equal length

Identification of a binding site by sequence conservation

Identification of a binding site by sequence conservation
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