A new hardware algorithm for searching genome patterns

The paper deals with a very hot problem concerning computation biology - the searching for a given reference pattern within a very long DNA chain. The software solutions in the field are limited by amount of resources and processing times. That is why complex programmable devices are more and more commonly used in the applications concerning microbiology. The paper presents the approach which is a modified Smith-Waterman dynamic programming methodology. The optimization of the entire algorithm and used resources has been done with respect of properties of FPGA components.