Prediction of Protein Coding Regions on a Programmable Vliw Architecture

Gene annotation is by nature a computationally intensive problem, as it needs to process huge data size of DNA sequences. This forces the need to look for alternate ways of implementing algorithms to predict exons. The paper presents a hardware-based approach in which a Digital Signal Processor is programmed to compute the computationally expensive part of the algorithm. The processor effectively exploits the 3-periodicity property exhibited by protein coding regions and indicates their presence in the sequence. Experimental results show superior performance when compared with implementation on a general purpose Intel processor for evaluating exons from DNA. This PCI pluggable card offers a great utility to scientists and engineers actively involved in indexing DNA sequences.