In the world of expanding set of biological species for various reasons, it requires high efficiency and memory to remember all the species so far found. If a new species have found and it is confirmed that it was not classified before, it is essential for the researchers to find out the family of species where it had been evolved. Thus researchers use various bioinformatics algorithms which deal with varying operations on biological data such as DNA analysis, Protein analysis, Genome information retrieval and Nucleotide applications. It is mandatory that the process of working on a DNA of a new species should be accurate and energy efficient. It should ensure the correctness of the solution. For an algorithm to work efficiently, a hardware implementation should be mapped into a platform which appreciates its inherent complexity and utilizes it completely. Biological algorithms have been often encountered with processes which require substantial parallel architecture. The best candidate would be Field Programmable Gate Arrays (FPGA) for the process of solving the biological mysteries satisfying the necessary requirements. In this paper, prominent algorithms for bioinformatics applications are studied and their FPGA implementation challenges and opportunities are explored. © Research India Publications.