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¶

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 pet28a vector — Plasmid map of a pet28a 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¶

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¶

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