Biotite
Python toolkit for sequence and structure bioinformatics on the platform.
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 plays for small molecules. See what you can achieve 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
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
Documentation: 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, which ships Biotite, or run them on your own machine.
FAQ
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PDB Search troubleshooting
Fix empty PDB searches, invalid or obsolete 4-character IDs, missing HETATM ligands in apo structures, altloc conformations, and RCSB timeouts.
Batch processing patterns
Run Biotite over many sequence or structure files — a timestamped run folder, xargs parallelism, per-file JSON outputs, retries that skip finished files.