Bioinformatics Language Benchmark

Overview:

This benchmark compares the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Needleman-Wunsch algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python.
A survey (bioinformatics.org) on which languages would be the most useful to learn ranked the following languages in decreasing order: Python, Perl, Java, C/C++ and the framework .NET which includes C#.


Features:

  • 6 programming languages: C, C++, C#, Java, Perl, Python
  • 3 programs: Needleman-Wunsch global alignment algorithm, Neighbor-Joining tree algorithm and BLAST parsing program.
  • 2 Operating Systems: Linux (Fedora) and Windows (XP)