Examples¶

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

Sequences¶

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Sequence logo of the Anderson promoter collection¶

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Pairwise sequence alignment of Avidin with Streptavidin¶

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Bionigma style multiple sequence alignment¶

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Dendrogram of the BLOSUM62 matrix¶

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Calculation of codon usage¶

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Biotite color schemes¶

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Biotite color schemes for protein sequences¶

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Homology of G-protein coupled receptors¶

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Hydropathy and conservation of HCN channels¶

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Multiple sequence alignment of Cas9 homologs¶

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Conservation of LexA DNA-binding site¶

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Sequence comparison of bacterial luciferases¶

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Feature map of a synthetic operon¶

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Identification of potential open reading frames¶

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Comparison of human PI3K family¶

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Plasmid map of a pet28a vector¶

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Visualization of a custom plasmid¶

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Quality of sequence reads¶

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Visualization of region in proximity to lac operon¶

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Mutual information as measure for coevolution of residues¶

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Domains of bacterial sigma factors¶

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Finding homologs of short sequences in a genome¶

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Polymorphisms in the THCA synthase gene¶

Structures¶

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Construction of an adjacency matrix¶

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Plotting the basepairs of a tRNA-like-structure¶

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Biological assembly of a structure¶

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Contact sites of protein-DNA interaction¶

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Calculation of protein diameter¶

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Detection of disulfide bonds¶

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Hydrogen bonds between protein domains¶

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Missing residues in protein structures of DNA-PKcs¶

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Visualization of glycosylated amino acids¶

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Superimposition of two protein structures¶

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Identification of lipid bilayer leaflets¶

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Basic analysis of a MD simulation¶

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Creating an MMTF based PDB archive¶

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MMTF as trajectory format¶

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Molecular visualization of caffeine¶

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Visualization of normal modes from an elastic network model¶

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Structural alignment of lysozyme variants using ‘Protein Blocks’¶

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Annual releases of PDB structures¶

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Assembly of a straight peptide from sequence¶

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Ramachandran plot of dynein motor domain¶

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Determination of amino acid enantiomers¶

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Creation of an amino acid rotamer library¶

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Solvation shells of sodium and chloride ions¶

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Secondary structure during an MD simulation¶

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Four ways to get the secondary structure of a protein¶

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