Abstract: Methods and systems for searching by computer for patterns in data are disclosed. These have particular, but not exclusive application to searching for target nucleotide sequences within a gene database. In the method can be performed by a computer that computer includes a central processing unit (CPU) that has one or more processing core, main memory accessible for read and write operations by the CPU, one or more graphics processing unit (GPU), and graphics memory accessible for read and write operations by the GPU. The method includes a step in which data to be processed as part of the pattern matching algorithm are transferred to the graphics memory, the GPU is operated to perform one or more processing step on the data. Following completion of the processing step, processed data are transferred from the graphics memory to the main memory. Algorithms that can be implemented using the invention include deterministic algorithms (e.g., Smith-Waterman) and non-deterministic algorithms (e.g., BLAST).