---
title: Biotite
description: Python toolkit for sequence and structure bioinformatics on the platform.
tags:
  - biotite
---

Biotite handles the sequence and structure bioinformatics groundwork — parsing FASTA, GenBank, and PDB/mmCIF files, fetching from biological databases, and running vectorized analysis in Python. Reach for it when you need to prepare, convert, or analyze biological sequences and structures in a reproducible job rather than compute small-molecule properties. It plays the same connective, workflow-preparing role for biomolecules that [RDKit](/docs/rdkit) plays for small molecules. See [what you can achieve](/docs/capabilities#chemistry) for the full set.

Biotite is a comprehensive open source **Python library for computational molecular biology**, developed to handle the complete bioinformatics workflow. Published in BMC Bioinformatics (2018, updated 2023), it provides unified tools for sequence and structural analysis with performance comparable to specialized single-purpose tools.

## Citations

> Kunzmann P, Hamacher K. Biotite: a unifying open source computational biology framework in Python. *BMC Bioinformatics*. 2018 Oct 1;19:346. doi: [10.1186/s12859-018-2367-z](https://doi.org/10.1186/s12859-018-2367-z)

> Kunzmann P, Müller TD, Greil M, Krumbach JH, Anter JM, Bauer D, Islam F, Hamacher K. Biotite: new tools for a versatile Python bioinformatics library. *BMC Bioinformatics*. 2023 Jun 5;24:236. doi: [10.1186/s12859-023-05345-6](https://doi.org/10.1186/s12859-023-05345-6)

> **Documentation**: [https://www.biotite-python.org](https://www.biotite-python.org)

## Key capabilities

- **Unified framework**: Four subpackages covering sequence, structure, database, and application interfaces
- **High performance**: Heavy use of NumPy for vectorized operations
- **Format support**: FASTA, GenBank, PDB/mmCIF, and compressed archives
- **Database integration**: Fetch from biological databases (NCBI, RCSB PDB, UniProt)

Use these guides to work with common file formats and run reproducible batch processing. The scripts in them are plain Biotite Python: ask Ivy to run them in the chat's [code workspace](/docs/sandbox), which ships Biotite, or run them on your own machine.

## FAQ

### Do I need to install Biotite?

  Not on the platform: the chat's [code workspace](/docs/sandbox) ships Biotite, so ask Ivy to run your analysis there. To run the scripts on your own machine, install it with `pip install biotite`.

### What data formats are supported?

  FASTA, GenBank, PDB/mmCIF for sequences and structures, plus compressed archives for batch runs.

### How do I troubleshoot missing dependencies?

  Pin Python 3.11+, install `biotite[full]`, and confirm required libs (OpenMM, DSSP) are present in your environment.

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