Public Databases: Retrieving and Manipulating Sequences for Beginners

This chapter outlines the basic requirements for finding and exploring sequences of interest in public databases, such as GenBank. As such, it is not aimed at experienced sequencers, for whom this will be “second nature,” but at the many clinical bacteriologists who rarely have need of DNA sequences in their usual work, and who would like to develop their interest in what can appear to be a daunting area. The topics discussed include finding and retrieving sequences from GenBank, identifying homologous sequences using BLAST searches, resources for accessing microbial genomes, and the Protein Data Bank. Finally, recommendations are made for useful software (freeware) and online sequence manipulation resources.