2012年1月27日星期五

A comparison of common programming languages used in bioinformatics - an old paper

 http://www.biomedcentral.com/1471-2105/9/82


Background

The performance of different programming languages has previously been benchmarked usingabstract mathematical algorithmsbut not using standard bioinformatics algorithmsWe comparedthe memory usage and speed of execution for three standard bioinformatics methods,implemented in programs using one of six different programming languagesPrograms for theSellers algorithmthe Neighbor-Joining tree construction algorithm and an algorithm for parsingBLAST file outputs were implemented in CC++, C#, JavaPerl and Python.

Results

Implementations in C and C++ were fastest and used the least memoryPrograms in theselanguages generally contained more lines of codeJava and Cappeared to be a compromisebetween the flexibility of Perl and Python and the fast performance of C and C++. The relativeperformance of the tested languages did not change from Windows to Linux and no clearevidence of a faster operating system was found.
Source code and additional information are available fromhttp://www.bioinformatics.org/benchmark/ webcite

Conclusion

This benchmark provides a comparison of six commonly used programming languages under two different operating systems. The overall comparison shows that a developer should choose an appropriate language carefully, taking into account the performance expected and the library availability for each language.

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