Biotite: a unifying open source computational biology framework in Python

• Published in: BMC bioinformatics Vol. 19; no. 1; pp. 346 - 8
• Main Authors: Kunzmann, Patrick, Hamacher, Kay
• Format: Journal Article
• Language: English
• Published: London BioMed Central 01.10.2018; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Accessibility; Algorithms; Aluminum Silicates; Analysis; Applications software; Bioinformatics; Biology; Biomedical and Life Sciences; Biotite; Computational Biology - methods; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Computer applications; Computer programs; Data processing; Ferrous Compounds; Fourier transforms; Interfaces; Life Sciences; Microarrays; Molecular biology; NumPy; Open source; Packaging; Parsers; Programming Languages; Proteins; Python; Python (Programming language); Sequence analysis; Software; Source code; Structural analysis; Structural biology; Open source; Sequence analysis; NumPy; Structural biology; Python
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-018-2367-z

Background As molecular biology is creating an increasing amount of sequence and structure data, the multitude of software to analyze this data is also rising. Most of the programs are made for a specific task, hence the user often needs to combine multiple programs in order to reach a goal. This can make the data processing unhandy, inflexible and even inefficient due to an overhead of read/write operations. Therefore, it is crucial to have a comprehensive, accessible and efficient computational biology framework in a scripting language to overcome these limitations. Results We have developed the Python package Biotite : a general computational biology framework, that represents sequence and structure data based on NumPy ndarrays . Furthermore the package contains seamless interfaces to biological databases and external software. The source code is freely accessible at https://github.com/biotite-dev/biotite . Conclusions Biotite is unifying in two ways: At first it bundles popular tasks in sequence analysis and structural bioinformatics in a consistently structured package. Secondly it adresses two groups of users: novice programmers get an easy access to Biotite due to its simplicity and the comprehensive documentation. On the other hand, advanced users can profit from its high performance and extensibility. They can implement their algorithms upon Biotite , so they can skip writing code for general functionality (like file parsers) and can focus on what their software makes unique.