Biopython: Python tools for computational biology

Abstract

The Biopython project was formed in August 1999 as a collaboration to collect and produce open source bioinformatics tools written in Python, an object-oriented scripting language. It is modeled on the highly successful Bioperl project, but has the goal of making libraries available for people doing computations in Python. The philosophy of all the Bio* projects is that part of bioinformaticists’ work involves software development. In order to prevent repeated efforts we believe that the field can be advanced more quickly if libraries that perform common programming functions were available. Thus, we hope to create a central source for high-quality bioinformatics tools that researchers can use.As an open source project, Biopython can be downloaded for free from the web site at http://www. biopython.org. Biopython libraries are currently under heavy development. This paper describes the current state of available Biopython tools, shows examples of their use in common bioinformatics problems, and describes plans for future development.