Many questions related to drug discovery and drug designs which are structure based can be answered using structural bioinformatics tools. A search of sequence databases followed by sequence alignment and analysis can easily answer questions related to the specificity of a particular target in a given organism. We isolate human DNA sequences, translate it into amino acids, then model a human protein structure based on the known structure of modal organism, which leads to discovering drugs that bonds the model proteins. In an alignment one may achieve better correspondence between two sequences if we allow gap in one of the sequences. In DNA sequence alignment various techniques are available. A method using binary sequence will be computational friendly. In this paper we provide a method of determining local and global DNA sequence alignment using binary matrix.