Skip to content

biotite-dev/biotite

master
Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
Code

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
doc
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Biotite at PyPI

Python version

Test status

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:

  • mdtraj - Required for trajetory file I/O operations.
  • matplotlib - Required for plotting purposes.

Biotite can be installed via Conda...

$ conda install -c conda-forge biotite

... or pip

$ pip install biotite

Usage

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---------------------
-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. Feel free to join or community chat on Discord.