BioNavigator is a web-based platform for sequence and structure analysis that integrates a large number of applications and databases under a streamlined, intuitive user interface. BioNavigator was designed not only for research but also as a platform for the practical teaching of sequence analysis, with a broad range of industry-standard applications accessible from multiple locations without the need to install specialized software. BioNavigator’s standardized interface enables students to concentrate on using programs rather than wasting time learning how to navigate each program’s interface. A range of educational features including course databases and step-by-step protocols complements the interface. In order to assist teachers wanting to introduce their students to sequence and structure analysis, a bioinformatics education package leveraging the BioNavigator interface was developed. This package includes a collection of protocols and practical bioinformatics problems to be used in practical classes in conjunction with BioNavigator.