New high-throughput techniques generate more and more data at an ever increasing pace. Large datasets introduce many problems for the computational biologists. Algorithm performance, memory management and visualization of complex data are amongst the biggest challenges. In this tutorial we will demonstrate how to address some of these issues within MATLAB. We will discuss characteristics of the MATLAB language that affect performance. We will look at how to apply tools such as profiling, nested functions, binary singleton expansion, and memory mapping, to improve the performance of functions. We will also look at some visualization methods to enable you to gain insight into large datasets.