We describe an open source, portable, JavaScript-based genome browser, JBrowse, that can be used to navigate genome annotations over the web. JBrowse helps preserve the user's sense of location by avoiding discontinuous transitions, instead offering smoothly animated panning, zooming, navigation, and track selection. Unlike most existing genome browsers, where the genome is rendered into images on the webserver and the role of the client is restricted to displaying those images, JBrowse distributes work between the server and client and therefore uses significantly less server overhead than previous genome browsers. We report benchmark results empirically comparing server-and client-side rendering strategies, review the architecture and design considerations of JBrowse, and describe a simple wiki plug-in that allows users to upload and share annotation tracks.[The JBrowse source code (freely licensed), live demonstrations, mailing list, documentation, bug-tracking, and virtual machine images are available at http://jbrowse.org/.]In a genome, spatial relationships often indicate functional relationships. A genome browser (Stein et al. 2002;Kent et al. 2003;Stalker et al. 2004) visually conveys the spatial relationships between different pieces of genomic data, helping users form hypotheses about their functional relationships. Current mainstream web-based genome browsers help users understand the genomic data within a given region, but hinder the further development of that understanding by requiring users to navigate to other regions page-by-page. These discontinuous page transitions impair the user's intuitive understanding of which genomic locus they are viewing and how the displayed data points relate to one another.A genome browser also allows a researcher to visually compare and correlate information from several different sources (Cline and Kent 2009); as such, it is a tool for evaluating multiple forms of evidence, looking at interesting biological cases, linking out to more detailed sources of information, such as genomic databases, communicating information to collaborators visually, preparing publication figures, and more. The availability of many genome browsers via the web allows scores of researchers to immediately dive into the data without the overhead of installing, configuring, or maintaining software, as well as provides the ability to link with a myriad of other web-based sources of information.Most current web-based genome browsers are implemented using the Common Gateway Interface (CGI) protocol, which provides a mechanism for a web server to generate a web page to send to the user. For example, GBrowse (Stein et al. 2002), a genome browser commonly used for model organism databases, consists of a set of Perl scripts and libraries stationed on the server side. These scripts query a server-side database of genomic features, render the HTML and graphics files needed to display a region of the genome, and transmit them to the browser along with HTML form-based navigation controls. To scroll the...
JBrowse is a web-based genome browser, allowing many sources of data to be visualized, interpreted and navigated in a coherent visual framework. JBrowse uses efficient data structures, pre-generation of image tiles and client-side rendering to provide a fast, interactive browsing experience. Many of JBrowse's design features make it well suited for visualizing high-volume data, such as aligned next-generation sequencing reads.
JBrowse is a Web‐based tool for visualizing genomic data. Unlike most other Web‐base genome browsers, JBrowse exploits the capabilities of the user's Web browser to make scrolling and zooming fast and smooth. It supports the browsers used by almost all Internet users, and is relatively simple to install. JBrowse can utilize multiple types of data in a variety of common genomic data formats, including genomic feature data in bioperl databases, GFF files, BED files, and quantitative data in wiggle files. This unit describes how to obtain the JBrowse software, set it up on a Linux or Mac OS X computer running as a Web server, and incorporate genome annotation data from multiple sources into JBrowse. After completing the protocols described in this unit, the reader will have a Web site that other users can visit to browse the genomic data. Curr. Protoc. Bioinform. 32:9.13.1‐9.13.13. © 2010 by John Wiley & Sons, Inc.
We performed benchmarks of phylogenetic grammar-based ncRNA gene prediction, experimenting with eight different models of structural evolution and two different programs for genome alignment. We evaluated our models using alignments of twelve Drosophila genomes. We find that ncRNA prediction performance can vary greatly between different gene predictors and subfamilies of ncRNA gene. Our estimates for false positive rates are based on simulations which preserve local islands of conservation; using these simulations, we predict a higher rate of false positives than previous computational ncRNA screens have reported. Using one of the tested prediction grammars, we provide an updated set of ncRNA predictions for D. melanogaster and compare them to previously-published predictions and experimental data. Many of our predictions show correlations with protein-coding genes. We found significant depletion of intergenic predictions near the 3′ end of coding regions and furthermore depletion of predictions in the first intron of protein-coding genes. Some of our predictions are colocated with larger putative unannotated genes: for example, 17 of our predictions showing homology to the RFAM family snoR28 appear in a tandem array on the X chromosome; the 4.5 Kbp spanned by the predicted tandem array is contained within a FlyBase-annotated cDNA.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.