https://github.com/biotite-dev/biotite

A comprehensive library for computational molecular biology
https://github.com/biotite-dev/biotite

bioinformatics computational-biology pdb-files sequence-analysis structural-biology

Last synced: 22 days ago
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A comprehensive library for computational molecular biology

• Host: GitHub
• URL: https://github.com/biotite-dev/biotite
• Owner: biotite-dev
• License: bsd-3-clause
• Created: 2017-07-30T12:18:33.000Z (over 8 years ago)
• Default Branch: main
• Last Pushed: 2026-01-01T12:36:48.000Z (about 1 month ago)
• Last Synced: 2026-01-03T15:25:53.521Z (about 1 month ago)
• Topics: bioinformatics, computational-biology, pdb-files, sequence-analysis, structural-biology
• Language: Python
• Homepage: https://www.biotite-python.org
• Size: 192 MB
• Stars: 911
• Watchers: 18
• Forks: 128
• Open Issues: 41
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE.rst

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• StarryDivineSky - biotite-dev/biotite

README

          
.. image:: https://img.shields.io/pypi/v/biotite.svg

   :target: https://pypi.python.org/pypi/biotite

   :alt: Biotite at PyPI

.. image:: https://img.shields.io/pypi/pyversions/biotite.svg

   :alt: Python version

.. image:: https://github.com/biotite-dev/biotite/actions/workflows/test_and_deploy.yml/badge.svg

   :target: https://github.com/biotite-dev/biotite/actions/workflows/test_and_deploy.yml

   :alt: Test status

.. image:: https://www.biotite-python.org/_static/assets/general/biotite_logo_m.png

   :alt: The Biotite Project

Biotite project

===============

*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:

| Kunzmann, P. & Hamacher, K. BMC Bioinformatics (2018) 19:346.

| ``_

Installation

------------

*Biotite* requires the following packages:

   - **numpy**

   - **requests**

   - **msgpack**

   - **networkx**

Some functions require some extra packages:

   - **matplotlib** - Required for plotting purposes.

*Biotite* can be installed via *Conda*...

.. code-block:: console

   $ conda install -c conda-forge biotite

... or *pip*

.. code-block:: console

   $ pip install biotite

Usage

-----

Here is a small example that downloads two protein sequences from the

*NCBI Entrez* database and aligns them:

.. code-block:: python

   import biotite.sequence.align as align

   import biotite.sequence.io.fasta as fasta

   import biotite.database.entrez as entrez

   # Download FASTA file for the sequences of avidin and streptavidin

   file_name = entrez.fetch_single_file(

       uids=["CAC34569", "ACL82594"], file_name="sequences.fasta",

       db_name="protein", ret_type="fasta"

   )

   # Parse the downloaded FASTA file

   # and create 'ProteinSequence' objects from it

   fasta_file = fasta.FastaFile.read(file_name)

   avidin_seq, streptavidin_seq = fasta.get_sequences(fasta_file).values()

   # Align sequences using the BLOSUM62 matrix with affine gap penalty

   matrix = align.SubstitutionMatrix.std_protein_matrix()

   alignments = align.align_optimal(

       avidin_seq, streptavidin_seq, matrix,

       gap_penalty=(-10, -1), terminal_penalty=False

   )

   print(alignments[0])

.. code-block::

   MVHATSPLLLLLLLSLALVAPGLSAR------KCSLTGKWDNDLGSNMTIGAVNSKGEFTGTYTTAV-TA

   -------------------DPSKESKAQAAVAEAGITGTWYNQLGSTFIVTA-NPDGSLTGTYESAVGNA

   TSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFS----ESTTVFTGQCFIDRNGKEV-LKTMWLLRSSVN

   ESRYVLTGRYDSTPATDGSGT--ALGWTVAWKNNYRNAHSATTWSGQYV---GGAEARINTQWLLTSGTT

   DIGDDWKATRVGINIFTRLRTQKE---------------------

   -AANAWKSTLVGHDTFTKVKPSAASIDAAKKAGVNNGNPLDAVQQ

More documentation, including a tutorial, an example gallery and the API

reference is available at ``_.

Contribution

------------

Interested in improving *Biotite*?

Have a look at the

`contribution guidelines `_.

Feel free to join our community chat on `Discord `_.