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
Bionigma style multiple sequence alignment
Dendrogram of the BLOSUM62 matrix
Biotite color schemes for protein sequences
Quantifying gene expression from RNA-seq data
Comparative genome assembly of SARS-CoV-2 B.1.1.7 variant
Genome comparison between chloroplasts and cyanobacteria
Finding homologs of a gene in a genome
Homology of G-protein coupled receptors
Hydropathy and conservation of HCN channels
Similarity of HCN and related channels
Multiple sequence alignment of Cas9 homologs
Conservation of LexA DNA-binding site
Statistics of local alignments and the E-value
Sequence comparison of bacterial luciferases
Feature map of a synthetic operon
Identification of potential open reading frames
Comparison of human PI3K family
Visualization of a custom plasmid
Plot epitope mapping data onto protein sequence alignments
Quality control of sequencing data
Identification of the ribosomal binding site
Visualization of region in proximity to lac operon
Mutual information as measure for coevolution of residues
Domains of bacterial sigma factors
Polymorphisms in the THCA synthase gene
Structures¶
Construction of an adjacency matrix
Plotting the base pairs of a tRNA-like-structure
Biological assembly of a structure
Contact sites of protein-DNA interaction
Calculation of protein diameter
Docking biotin to streptavidin
Hydrogen bonds between protein domains
Missing residues in protein structures of DNA-PKcs
Visualization of glycosylated amino acids
Superimposition of two protein structures
Identification of lipid bilayer leaflets
Basic analysis of a MD simulation
Creating an MMTF based PDB archive
Molecular visualization of caffeine
Visualization of normal modes from an elastic network model
Structural alignment of lysozyme variants using ‘Protein Blocks’
Annual releases of PDB structures
Assembly of a straight peptide from sequence
Ramachandran plot of dynein motor domain
Determination of amino acid enantiomers
Creation of an amino acid rotamer library
Solvation shells of sodium and chloride ions
Secondary structure during an MD simulation
Comparison of a tRNA-like-structure with a tRNA
Four ways to get the secondary structure of a protein
Cavity solvation in different states of HCN4
Visualization of Watson-Crick base pairs