A comparison of common programming languages used in bioinformatics.

ABSTRACT:

Background

The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared 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 Sellers 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.

Results

Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast per

SUBMITTER: Fourment M 

PROVIDER: S-EPMC2267699 | biostudies-literature | 2008 Feb

REPOSITORIES: biostudies-literature