WinBioinfTools: Bioinformatics tools for Windows cluster

Open source bioinformatics tools running under MS Windows are rare to find, and those running under Windows HPC cluster are almost non-existing, in spite of the fact that Windows is the most popular operating system. Therefore, we introduce WinBioinfTools, an open source toolkit containing a number of bioinformatics tools running under Windows High Performance Computing Server 2008. The current version contains three programs for biological sequence analysis: 1) CoCoNUT for pairwise genome comparison, 2) WinBLAST for biological database search, and 3) WinPSA for global pairwise sequence alignment. We show how the Linux/Unix components of these programs were ported to run under Windows. We also demonstrate by experiments the advantage of using a computer cluster compared to a single machine, highlighting the benefits of using the Windows HPC Cluster 2008. Furthermore, we compare the performance of WinBioinfTools on the Windows- and Linux cluster.