A flood of data means that many of the challenges in biology are now challenges in computing. Bioinformatics, the application of computational techniques to analyse the information associated with biomolecules on a large-scale, has now firmly established itself as a discipline in molecular biology, and encompasses a wide range of subject areas from structural biology, genomics to gene expression studies. In this text we provide an introduction and overview of the current state of the field. We discuss the main principles that underpin bioinformatics analyses, look at the types of biological information and databases that are commonly used, and finally examine some of the studies that are being conducted, particularly with reference to transcription regulatory systems. The aims of bioinformatics are threefold. First, at its simplest bioinformatics organises data in a way that allows researchers to access existing information and to submit new entries as they are produced, e.g. the Protein Data Bank for 3D macromolecular structures . While data-curation is an essential task, the information stored in these databases is essentially useless until analysed. Thus the purpose of bioinformatics extends much further. The second aim is to develop tools and resources that aid in the analysis of data. For example, having sequenced a particular protein, it is of interest to compare it with previously characterised sequences. This needs more than just a simple text-based search and programs such as FASTA and PSI-BLAST must consider what comprises a biologically significant match. Development of such resources dictates expertise in computational theory as well as a thorough understanding of biology. The third aim is to use these tools to analyse the data and interpret the results in a biologically meaningful manner. Traditionally, biological studies examined individual systems in detail, and frequently compared them with a few that are related. In bioinformatics, we can now conduct global analyses of all the available data with the aim of uncovering common principles that apply across many systems and highlight novel feature.