The understanding of gene regulation is the most basic need for the classification of genes within a DNA. These genes within the DNA are grouped together into clusters also known as Transcription Units. The genes are grouped into transcription units for the purpose of construction and regulation of gene expression and synthesis of proteins. This knowledge further contributes as essential information for the process of drug design and to determine the protein functions of newly sequenced genomes. It is possible to use the diverse biological information across multiple genomes as an input to the classification problem. The purpose of this work is to show that Particle Swarm Optimization may provide for more efficient classification as compared to other algorithms. To validate the approach E.Coli complete genome is taken as the benchmark genome.