Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking

Abstract

Background: The Bluejay genome browser has been developed over several years to address the challenges posed by the ever increasing number of data types as well as the increasing volume of data in genome research. Beginning with a browser capable of rendering views of XML-based genomic information and providing scalable vector graphics output, we have now completed version 1.0 of the system with many additional features. Our development efforts were guided by our observation that biologists who use both gene expression profiling and comparative genomics gain functional insights above and beyond those provided by traditional per-gene analyses.

Results: Bluejay 1.0 is a genome viewer integrating genome annotation with: (i) gene expression information; and (ii) comparative analysis with an unlimited number of other genomes in the same view. This allows the biologist to see a gene not just in the context of its genome, but also its regulation and its evolution. Bluejay now has rich provision for personalization by users: (i) numerous display customization features; (ii) the availability of waypoints for marking multiple points of interest on a genome and subsequently utilizing them; and (iii) the ability to take user relevance feedback of annotated genes or textual items to offer personalized recommendations. Bluejay 1.0 also embeds the Seahawk browser for the Moby protocol, enabling users to seamlessly invoke hundreds of Web Services on genomic data of interest without any hard-coding.

Conclusion: Bluejay offers a unique set of customizable genome-browsing features, with the goal of allowing biologists to quickly focus on, analyze, compare, and retrieve related information on the parts of the genomic data they are most interested in. We expect these capabilities of Bluejay to benefit the many biologists who want to answer complex questions using the information available from completely sequenced genomes.

Figure 1

Conceptual structure of Bluejay 1.0. Bluejay can load XML and non-XML genome annotation data, which are internally represented as an XML document, with XLinks inserted. The user interacts with Bluejay through the browser GUI, which communicates with the comparison module, customization modules, embedded applications, and gene annotation pages.

Figure 2

Bacterial genome comparison. The comparison of two bacterial genomes (Chlamydia trachomatis and Chlamydia muridarum) shows that they share many genes, which belong to the same Gene Ontology (GO) classification, as indicated by the linking lines. Only those links with an angular distance less than 2% of 360 degrees are shown.

Figure 3

Human chromosome comparison. The comparison of human chromosomes 17q, 12, 7, and 2q shows that many gene families, such as homeobox (HOX) and epidermal growth factor receptor (ErbB) genes, are duplicated on several chromosomes.

Figure 4

Hybrid recommender and personalized search. A matched item from the search engine is ranked, based on previously learned user preferences, and then refined by the system's knowledge of its importance. An example: (a) A search for "oxidoreductase"' is performed on the Sulfolobus solfataricus genome; (b) The relevance for each search item is listed in the Relevance column. Items containing "Fe-S" have the highest relevance due to TF-IDF ranking. The user subsequently rates items containing Fe-S low (1) and items containing NADH high (5) using the Feature Rating column (rating action not shown); (c) In a subsequent search for oxidoreductase, the items containing NADH are rated above those containing Fe-S, based on the user profile.

Figure 5

Customized navigation using waypoints. The user sets two waypoints and zooms in the area around Waypoint2 (top). The selected area is displayed in greater detail, then the user clicks Waypoint1 in the "Waypoints" tab (middle). The focus changes to Waypoint1, then the user selects "Edit Waypoint" action (bottom) to change the attributes.