Gene transcription regulation impacts the final expression of gene. Generally gene expression is regulated via an interaction between regulatory proteins and specific DNA elements. If we find out the binding site of regulatory factors, we could un-derstand the mechanism of control of gene transcription more. For this reason, it is a very important issue to find out the regulatory factors of gene transcription. In this thesis, we try to find out the regulatory protein binding sites from the comparisons of DNA sequence and scoring matrices with suitable bio-conditions. The steepest ascent algorithm is adopted to search the possible locations of binding sites. The predicted results of regulatory protein binding sites are displayed with table and charts. The proposed system in this thesis will help the biologists to analyze the regu-latory protein binding sites efficiently, and to develop effective drugs for genetic dis-eases.
