Many questions that biologists want to answer using the information available from completely sequenced genomes are complex. A graphical environment allows users to visually explore and operate on a sequence. Sequence and annotation data exists in bewildering varieties of types and levels of detail. The graphical environment therefore needs to adapt to this variation to provide the user the best possible visual representation of genomic data in a given context. As more and more online tools and services become available for biologists, mediating software should also be able to integrate and link to them. The Bluejay browser is a Java-based visual environment for exploring biological sequences. Uniquely, Bluejay fully integrates existing gene expression software into a genomic context. Bluejay also differentiates itself from most form-based HTML sequence browsers because it: (i) is highly scalable so that it can visualize a wide range of genomic objects ranging from a large whole genome down to individual nucleotides by using data-transformational Web services; and (ii) dynamically discovers and provides links to disparate resources such as gene annotation data (via XLinks) and semantically-described biological Web Services (via the BioMOBY protocol).