Data on genome structural and functional features for various organisms are being accumulated and analyzed in laboratories all over the world. The data are stored and analyzed on a large variety of expert systems. The public access to most of these data offers to scientists around the world an unprecedented chance to data mine and explores in depth this extraordinary information repository, trying to convert data into knowledge. The DNA and RNA molecules are symbolic sequences of amino acids in the corresponding proteins has definite advantages in what concerns storage, search, and retrieval of genomic information. In this study an attempt is made to develop an algorithm for aligning multiple DNA / protein sequences. In this process hotspots are located in a protein sequence using the multiple sequence alignment.