Promoter Sequence Analysis through No Gap Multiple Sequence Alignment of Motif Pairs

The advancement in the sequencing technology has led to exponential increase in the biological sequence data. Therefore the need for methods and techniques that analyze this sequence data are in demand. A central task in analysis of this data is sequence alignment. In this work, we present a new multiple sequence alignment method for analyzing the similarity/homology existing in the promoter sequences. We extract the motif pair feature from the binarized position specific motif matrix (PSMM) of each promoter pair or sets. We then compare the count of motif pairs between the promoter sequences to find the similarity. The efficacy of the proposed method is tested on two datasets obtained from NCBI. The results obtained agree with our understanding of organism similarity.