  Open source bioinformatics tools running under MS Windows are rare to find,
and those running under Windows HPC cluster are almost non-existing. This is
despite the fact that the Windows is the most popular operating system used
among life scientists. Therefore, we introduce in this initiative
WinBioinfTools, a toolkit containing a number of bioinformatics tools running
under Windows High Performance Computing Server 2008. It is an open source code
package, where users and developers can share and add to. We currently start
with three programs from the area of sequence analysis: 1) CoCoNUT for pairwise
genome comparison, 2) parallel BLAST for biological database search, and 3)
parallel global pairwise sequence alignment. In this report, we focus on
technical aspects concerning how some components of these tools were ported
from Linux/Unix environment to run under Windows. We also show the advantages
of using the Windows HPC Cluster 2008. We demonstrate by experiments the
performance gain achieved when using a computer cluster against a single
machine. Furthermore, we show the results of comparing the performance of
WinBioinfTools on the Windows and Linux Cluster.
