Abstract
BackgroundThe Distributed Annotation System (DAS) offers a standard protocol for sharing and integrating annotations on biological sequences. There are more than 1000 DAS sources available and the number is steadily increasing. Clients are an essential part of the DAS system and integrate data from several independent sources in order to create a useful representation to the user. While web-based DAS clients exist, most of them do not have direct interaction capabilities such as dragging and zooming with the mouse.ResultsHere we present GenExp, a web based and fully interactive visual DAS client. GenExp is a genome oriented DAS client capable of creating informative representations of genomic data zooming out from base level to complete chromosomes. It proposes a novel approach to genomic data rendering and uses the latest HTML5 web technologies to create the data representation inside the client browser. Thanks to client-side rendering most position changes do not need a network request to the server and so responses to zooming and panning are almost immediate. In GenExp it is possible to explore the genome intuitively moving it with the mouse just like geographical map applications. Additionally, in GenExp it is possible to have more than one data viewer at the same time and to save the current state of the application to revisit it later on.ConclusionsGenExp is a new interactive web-based client for DAS and addresses some of the short-comings of the existing clients. It uses client-side data rendering techniques resulting in easier genome browsing and exploration. GenExp is open source under the GPL license and it is freely available at http://gralggen.lsi.upc.edu/recerca/genexp.
Highlights
In recent years the volume of genomic data on genome sequences and their annotations have been growing at a rapid pace
Our genome browser GenExp -available at http://gralggen.lsi. upc.edu/genexp- offers a web-based ready-to-use interactive genome browsing experience and leverages the richness of the genomic Distributed Annotation System (DAS) data sources with the ease of web applications
Overview As a genome oriented DAS client, GenExp is able to display data coming from the available genomic DAS sources in an integrated way, creating a single representation with data from different sources represented side-by-side and precisely positioned over its common reference sequence
Summary
In recent years the volume of genomic data on genome sequences and their annotations have been growing at a rapid pace. New organisms are sequenced every year, annotations on those sequences are constantly produced and refined and new data associated with these annotations is created. Most of this data is stored in public databases which are freely accessible and usually offer various options to browse and download the data, most of them via web interfaces. The DAS system provides a standard programmatic interface that is relatively easy to implement. This is specially important for small databases that lack the resources to develop and maintain such a system. While web-based DAS clients exist, most of them do not have direct interaction capabilities such as dragging and zooming with the mouse
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call