Biotite documentation

The Biotite package bundles popular tools in computational biology into an unifying framework. It offers file I/O operations, analyses and manipulations for biological sequence and structure data. Furthermore, the package provides interfaces for popular biological databases and external software.

The internal structure and sequence representations are based on NumPy ndarrays, taking the advantage of C-accelerated operations. Time consuming operations that could not be vectorised are mostly implemented in Cython in order to achieve C-accelerations in those places, too.

Additionally the package aims for simple usability and extensibility: The objects representing structures and sequences can be indexed and scliced like an ndarray. Even the actual internal ndarrays are easily accessible allowing advanced users to implement their own algorithms upon the existing types.

Subpackages

Biotite currently consists of 4 subpackages:

Sequence

The sequence subpackage contains functionality for working with sequence information of any kind. The package contains by default sequence types for nucleotides and proteins, but the alphabet-based implementation allows simple integration of own sequence types, even if they do not rely on letters. Beside the standard I/O operations, the package includes general purpose functions for sequence manipulations and global/local alignments.

Structure

The structure subpackage enables handling of 3D structures of biomolecules. Simplified, a structure is represented by a list of atoms and their properties, based on ndarrays. The subpackage includes read/write functionality for different formats, structure filters, coordinate transformations, angle and bond measurements, accessible surface area calculation, structure superimposition and more.

Database

The database subpackage is all about downloading data from biological databases, including the probably most important ones: the RCSB PDB and the NCBI Entrez database.

Application

The application subpackage provides interfaces for external software. The interfaces range from locally installed software (e.g. MSA software) to web apps (e.g. BLAST). The speciality is that the interfaces are seamless: You do not have to write input files and read output files, you only have to input Python objects and you get Python objects. It is basically very similar to using normal Python functions.