Pairwise DNA and protein sequence alignment is an important task in bioinformatics which forms the basis of many other tasks like multiple sequence alignment, protein structure and function prediction, phylogenetic analysis. In general, more emphasis is given to protein sequence alignment, and the alignment methods designed for protein sequences can usually be used with little modification for DNA sequences as well. However, it is desirable to design methods specifically for DNA alignments, making use of specific DNA sequence models and if possible, also of the specific sequences being aligned. In this paper, we present an iterative method for DNA sequence alignment with sequence specific transition-transversion ratio. Preliminary experiments indicate that the proposed technique has significant potential. The approach better suits to the nature of the specific DNA sequence pair, and could be a significant step in the direction of using sequence specific substitution matrices for DNA sequences.