The popular technologies, internet computing and Grid technologies promise to change the way we tackle complex problems. They will enable large-scale aggregation and sharing of computational, data and other resources across institutional boundaries. And harnessing these new technologies effectively will transform scientific disciplines ranging from high-energy physics to the life sciences. The computational analysis of biological sequences is a kind of computation driven science. Cause the biology data growing quickly and these databases are heterogeneous. We can use the grid system sharing and integrating the heterogeneous biology database. As we know, bioinformatics tools can speed up analysis the large-scale sequence data, especially about sequence alignment and analysis. The FASTA is a tool for aligning multiple protein or nucleotide sequences. These two bioinformatics software which we used is a distributed and parallel version. The software uses a message-passing library called MPI (Message Passing Interface) and runs on distributed workstation clusters as well as on traditional parallel computers. A grid computing environment is proposed and constructed on multiple Linux PC Clusters by using Globus Toolkit (GT) and SUN Grid Engine (SGE). The experimental results and performances of the bioinformatics tool using on grid system are also presented in this paper.