Computational Tools and Resources in Plant Genome Informatics

Though all biologists deal with information, only recently have the computational challenges of systematically collecting, storing, organising, manipulating visualising and analysing large amounts of biological information come to be widely appreciated. The cause of this is the explosive growth of genomics. The term bioinformatics was originally coined for the application of information technology to large volumes of biological, and particularly genomic, data. The field of bioinformatics has come to be intermingled with traditional computational biology and biostatistics, which are strictly concerned not with how to handle the information itself, but rather how to extract biological meaning from it. Thus, bioinformatics, in its broad sense, can be seen as providing both the infrastructure and the scientific framework in which biologists take information and use computers to help convert it into knowledge. Despite the relative youth of the field as a recognised discipline, there is an impressive diversity of bioinformatics resources currently available. By necessity, we only focus on a small slice of this diversity here. We pay particular attention to sequence analysis because of its centrality to genomics. We also do not attempt to provide specific protocols, as the specific needs of users vary greatly. The resources we describe range drastically in sophistication from little tested programs posted on graduate student web pages to very stable and complex databases maintained by governmental agencies. The better ones typically provide manuals and tutorials, often containing descriptions of the underlying principles. The reader is strongly advised to consult the documentation available for each tool. Though a wide array of commercial resources exist, some of which are ideally suited to specific tasks, many of the most fundamental and longlived bioinformatics tools are freely available. For this reason, we describe primarily non-commercial software in this chapter. Many of the databases and analysis tools we describe are hosted by government or academic research centres and can be accessed via user-friendly web interfaces. Tables 4.1 and 4.2 list the Uniform Resource Locators (URLs) for all the online resources that are discussed in the text.