Biotite documentation

Biotite is your Swiss army knife for bioinformatics. Whether you want to identify homologous sequence regions in a protein family or you would like to find disulfide bonds in a protein structure: Biotite has the right tool for you. This package bundles popular tasks in computational molecular biology into a uniform Python library. It can handle a major part of the typical workflow for sequence and biomolecular structure data:

  • Searching and fetching data from biological databases

  • Reading and writing popular sequence/structure file formats

  • Analyzing and editing sequence/structure data

  • Visualizing sequence/structure data

  • Interfacing external applications for further analysis

Biotite internally stores most of the data as NumPy ndarray objects, enabling

  • fast C-accelerated analysis,

  • intuitive usability through NumPy-like indexing syntax,

  • extensibility through direct access of the internal NumPy arrays.

As a result the user can skip writing code for basic functionality (like file parsers) and can focus on what their code makes unique - from small analysis scripts to entire bioinformatics software packages.

If you use Biotite in a scientific publication, please cite:


P. Kunzmann, K. Hamacher, "Biotite: a unifying open source computational biology framework in Python," BMC Bioinformatics, vol. 19, pp. 346, October 2018. doi: 10.1186/s12859-018-2367-z