Examples

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

Sequences

Sequence logo of the Anderson promoter collection

Sequence logo of the Anderson promoter collection

Pairwise sequence alignment of Avidin with Streptavidin

Pairwise sequence alignment of Avidin with Streptavidin

Bionigma style multiple sequence alignment

Bionigma style multiple sequence alignment

Dendrogram of the BLOSUM62 matrix

Dendrogram of the BLOSUM62 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

Comparative genome assembly of SARS-CoV-2 B.1.1.7 variant

Comparative genome assembly of SARS-CoV-2 B.1.1.7 variant

Genome comparison between chloroplasts and cyanobacteria

Genome comparison between chloroplasts and cyanobacteria

Finding homologs of a gene in a genome

Finding homologs of a gene in a genome

Homology of G-protein coupled receptors

Homology of G-protein coupled receptors

Hydropathy and conservation of HCN channels

Hydropathy and conservation of HCN channels

Similarity of HCN and related channels

Similarity of HCN and related channels

Multiple sequence alignment of Cas9 homologs

Multiple sequence alignment of Cas9 homologs

Conservation of LexA DNA-binding site

Conservation of *LexA* DNA-binding site

Statistics of local alignments and the E-value

Statistics of local alignments and the E-value

Sequence comparison of bacterial luciferases

Sequence comparison of bacterial luciferases

Feature map of a synthetic operon

Feature map of a synthetic operon

Identification of potential open reading frames

Identification of potential open reading frames

Comparison of human PI3K family

Comparison of human PI3K family

Plasmid map of a pET15 vector

Plasmid map of a pET15 vector

Visualization of a custom plasmid

Visualization of a custom plasmid

Quality control of sequencing data

Quality control of sequencing data

Identification of the ribosomal binding site

Identification of the ribosomal binding site

Quality of sequence reads

Quality of sequence reads

Visualization of region in proximity to lac operon

Visualization of region in proximity to *lac* operon

Mutual information as measure for coevolution of residues

Mutual information as measure for coevolution of residues

Domains of bacterial sigma factors

Domains of bacterial sigma factors

Polymorphisms in the THCA synthase gene

Polymorphisms in the THCA synthase gene

Structures

Construction of an adjacency matrix

Construction of an adjacency matrix

Enumeration of alkane isomers

Enumeration of alkane isomers

Plotting the base pairs of a tRNA-like-structure

Plotting the base pairs of a tRNA-like-structure

Biological assembly of a structure

Biological assembly of a structure

Contact sites of protein-DNA interaction

Contact sites of protein-DNA interaction

Calculation of protein diameter

Calculation of protein diameter

Detection of disulfide bonds

Detection of disulfide bonds

Docking biotin to streptavidin

Docking biotin to streptavidin

Hydrogen bonds between protein domains

Hydrogen bonds between protein domains

Missing residues in protein structures of DNA-PKcs

Missing residues in protein structures of DNA-PKcs

Visualization of glycosylated amino acids

Visualization of glycosylated amino acids

Superimposition of two protein structures

Superimposition of two protein structures

Identification of lipid bilayer leaflets

Identification of lipid bilayer leaflets

Leontis-Westhof Nomenclature

Leontis-Westhof Nomenclature

Basic analysis of a MD simulation

Basic analysis of a MD simulation

Creating an MMTF based PDB archive

Creating an MMTF based PDB archive

MMTF as trajectory format

MMTF as trajectory format

Molecular visualization of caffeine

Molecular visualization of caffeine

Visualization of normal modes from an elastic network model

Visualization of normal modes from an elastic network model

Structural alignment of lysozyme variants using ‘Protein Blocks’

Structural alignment of lysozyme variants using 'Protein Blocks'

Annual releases of PDB structures

Annual releases of PDB structures

Partial charge distribution

Partial charge distribution

Assembly of a straight peptide from sequence

Assembly of a straight peptide from sequence

Ramachandran plot of dynein motor domain

Ramachandran plot of dynein motor domain

Determination of amino acid enantiomers

Determination of amino acid enantiomers

Creation of an amino acid rotamer library

Creation of an amino acid rotamer library

Arrangement of beta-sheets

Arrangement of beta-sheets

Solvation shells of sodium and chloride ions

Solvation shells of sodium and chloride ions

Secondary structure during an MD simulation

Secondary structure during an MD simulation

Comparison of a tRNA-like-structure with a tRNA

Comparison of a tRNA-like-structure with a tRNA

Four ways to get the secondary structure of a protein

Four ways to get the secondary structure of a protein

Cavity solvation in different states of HCN4

Cavity solvation in different states of HCN4

Visualization of Watson-Crick base pairs

Visualization of Watson-Crick base pairs