Chapter 12. Hardware and Software Optimizations

This chapter explores how to optimize BLAST searches for maximum throughput and will help you get the most out of your current and future hardware and software. The first rule of BLAST performance is optimize your BLAST parameters. Incorrect settings can cause BLAST to run slowly, and you can often achieve surprising increases in speed by adjusting a parameter or two. Chapter 9 can help you choose the correct parameters for a particular experiment. If you're already running BLAST efficiently and want to get the most BLAST performance possible, read on.