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The southern cattle tick, Rhipicephalus microplus, is an economically important tick that can transmit several pathogenic microorganisms, including babesiosis and anaplasmosis, to its cattle and white tailed deer hosts during the feeding process. While a campaign led by the U.S. Department of Agriculture (USDA) resulted in the eradication of the tick in the United States, many factors have contributed to its re-emergence in Texas, thus leading to the need for a vaccine to protect livestock from these diseases. This study employed a bioinformatic analysis pipeline to identify potential vaccine targets from a variety of assembled Rhipicephalus microplus EST sequences. Potential tick peptides were predicted and compared to Homo sapien, Drosophila melanogaster and Bos taurus proteomes to identify proteins unique to ticks. These proteins serve as possible targets in the development of a vaccine to combat the re-emergence of Rhipicephalus microplus in the United States cattle industry.