Computer generated sequence alignment has become a conventional tool in bioinformatics. One method of determining similarity between two sequences is through a pair-wise sequence alignment. Since Smith-Waterman proposed the optimal sequence alignment algorithm in 1981, many local sequence alignment tools have adopted this algorithm for their alignment engine. However, most of the conventional tools lack the ability of incorporating biological properties into the alignment result which often leads to incorrect alignment. In this paper, we introduce a pair-wise alignment system called INSPAL (Information Specific Algorithm) that incorporates biological properties into the algorithm so that it can suggest an appropriate sequence alignment based on the given proteins. Experimental comparisons with two popular tools ALIGN and SIM indicate good performance of INSPAL.