We present a new web-based genomics browser with novel rendering and annotation capabilities designed to overcome some of the shortcomings in available approaches. Most of the popular current browsers use on-the-fly server-side rendering of tracks and features which is not efficient in terms of performance or scalability. In addition, these browsers often rely on very specific library dependencies, where writing plugins or modifying existing code can be troublesome and resource expensive. We focus on functionality which in many cases is available in existing tools but with an improved and more productive user interface. Responsiveness: Server side caching and client side rendering based on JSON generated from server responses, helps to decrease the server load compared to server-side rendering browsers, and improves the user browsing experience. Availability • TGAC Browser has been released to community and is available in variety of ways, including source code. We would be pleased to help any potential users and developers interested in the project. • Information about the TGAC Browser and a demo instance please visit : http://tgac-browser.tgac.ac.uk • Follow on @TGACBrowser • TGAC Browser source code available at: https://github.com/TGAC/TGACBrowser User-friendly Browser Interaction: Traversing the reference genome, adding/removing tracks, drag and drop selections are examples of actions that are seamlessly powered by modern web browsers. In addition, other key features of the TGAC browser include merging and removing tracks and exporting sequences in FASTA format. Analysis Integration: Ability to carry out alignments using tools such BLAST is a feature supported by TGAC Browser with a novel interface. User Annotation: The TGAC Browser accepts user-defined annotations which can be persisted on the server and reloaded and shared at a later date. Off-the-shelf Installation: The prerequisites are Tomcat server and a standard Ensembl backend database to host sequence annotations and the TGAC Browser is ready to be used. Features Implementation • The Ensembl database schema underpins the TGAC Browser. • Ensembl database exposed to frontend with Java SQL data access objects. Data transfered to client via JSON and generates graphics via web browser JavaScript libraries. • We use property files so the TGAC Browser can be customised by editing a simple text file. • We use the jQuery, a JavaScript library and d3.js to generate interactive visualisations on the browser. • TGAC Browser can be customised to perform BLAST on local machine, NCBI or HPC cluster to make it faster for more users. 1. Database information: from meta_data 2. Easy Search: Search with reference, gene name, gene attributes, etc 3. BLAST Search: Integrates BLAST to search for sequence of interest 4. User Sessions: TGAC Browser supports user sessions 5. Assembly tracks 6. A standard gene track 7. Controls 8. Genomic Map with markers 2 3 4
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