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:
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…
$ conda install -c conda-forge biotite… or pip
$ pip install biotiteUsage
Here is a small example that downloads two protein sequences from the NCBI Entrez database and aligns them:
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])MVHATSPLLLLLLLSLALVAPGLSAR------KCSLTGKWDNDLGSNMTIGAVNSKGEFTGTYTTAV-TA
-------------------DPSKESKAQAAVAEAGITGTWYNQLGSTFIVTA-NPDGSLTGTYESAVGNA
TSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFS----ESTTVFTGQCFIDRNGKEV-LKTMWLLRSSVN
ESRYVLTGRYDSTPATDGSGT--ALGWTVAWKNNYRNAHSATTWSGQYV---GGAEARINTQWLLTSGTT
DIGDDWKATRVGINIFTRLRTQKE---------------------
-AANAWKSTLVGHDTFTKVKPSAASIDAAKKAGVNNGNPLDAVQQMore 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. Feel free to join our community chat on Discord.
2 maintainers
Release files for biotite 1.7.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| biotite-1.7.1.tar.gz | 39.9 MB | Details |
Built distributions (wheels)
Total release size: 658.2 MB
Release files / biotite-1.7.1.tar.gz
| Download URL | biotite-1.7.1.tar.gz |
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