The bioinformatics field confronts exponential growth of data and increasing problem complexity. Recent progress in computing and data Grid are highlighted as an approach to handle these situations. The simplified usage of Grid computing resources and the fault-tolerance of large data placement in bioinformatics analysis are the main keys for taking advantage of Grid technology. For the purpose of achieving Grid computing jobs, we have already provided a model of problem solving environment for integrated bioinformatics solution on Grid supporting process manager. Here we have additionally developed BioGrid Problem Solving Environment (BioGridPSE) as an updated version that guarantees both the completion of computational jobs and data placement jobs in the Grid and supports flexible process design for bioinformatics analysis, user customized interface generation, and programmable data parsing. The efficiency and usability of BioGridPSE have been tested with high-throughput and complex bioinformatics analysis such as whole genome global alignment.