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:alt: Biotite at PyPI
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:alt: Python version
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: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/contribute.html>
.
Feel free to join our community chat on Discord <https://discord.gg/cUjDguF>
.