The BLAST is the sequence comparison strategy mostly used in computational biology. Therefore, research on data structures, secondary memory access methods and on the algorithm itself, could bring important optimizations and consequently contributions to the area. In this work, we study a NCBI BLAST version by analyzing its data structures and algorithms for data manipulating. In addition, we collect performance data for identifying processing bottleneck in all the BLAST execution phases. Based on this analysis, data compress techniques were applied as a strategy for reducing number of secondary memory access operations. Finally, a modified version of BLAST was implemented in the Microsoft Windows environment, where the program was directly altered. Finally, an analysis was made over using the results of execution of original BLAST against modified BLAST.