biotite

.. 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. | <https://doi.org/10.1186/s12859-018-2367-z>_

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 <https://www.biotite-python.org/>_.

Contribution

Interested in improving Biotite? Have a look at the contribution guidelines <https://www.biotite-python.org/latest/contribution/index.html>. Feel free to join our community chat on Discord <https://discord.gg/cUjDguF>.