For biologists very hard time is with analyzing the uniqueness between two sample sequences such as DNA, RNA and protein sequences. A Bio- sequence represents a single, continuous molecule of nucleic acid or protein. It can be anything from a band on a gel to a complete chromosome. That's to design for a huge database system which finds similarities between two sequences that have biological significance. In such condition we have to compromise in computation time, this can be overcome through implementation BLASTN process. In this paper the BLAST process will be working more efficient by a new approach for biological sequence database scanning. The scanning is performed with reconfigurable FPGA base hardware by comparing sequence one to many sequences from the database. The experimental sequence matching reduces the computation time of BLAST