This research was mainly concerned with the feasibility of the possible use of RNA structure energies in genome sequence search. The primary objective of this research was to determine if there exists a correlation between the energy required to anneal two nucleotide strands and the BLAST score associated with these strands. A total of 153 (back-translated) proteins and RNA sequences were used. A BLAST search of GenBank was performed for each of the 153 sequences and all resulting alignments were used to compute the corresponding energy value. The total resulting alignments were 38,995. Results reveal that there is a statistically significant linear correlation between BLAST scores and the corresponding RNA secondary structure energies. The average R-value was determined to be 0.91 and the boundary statistical probability of exceeding R was determined to be 0.001. In addition, the energy rules appear to be more sensitive and generalized than the BLAST scoring scheme.