Non-Von Neumann computer architectures are being explored for acceleration of difficult problems. The Automata Processor is a unique non Von Neumann architecture capable of efficient modeling and execution of non-deterministic finite automata. The Automata Processor is shown to be excellent in string comparison operations, specifically with regard to bioinformatics problems. A greatly accelerated solution for Prosite pattern matching using the Automata Processor called PROTOMOTA is presented. Furthermore, a developers' guide detailing the lessons learnt while designing and implementing PROTOMOTA is provided. It is hoped that the developers' guide would aid future developers to avoid critical pitfalls, while exploiting the capabilities of the Automata Processor to the fullest.