Title page for ETD etd-04302012-125308


Type of Document Master's Thesis
Author Whisenhunt, Phillip J
Author's Email Address pjw@vt.edu
URN etd-04302012-125308
Title NextBrowse: An integrated and interactive web-based genome browser for analyzing and interpreting genomic data
Degree Master of Science
Department Computer Science
Advisory Committee
Advisor Name Title
Mittelman, David Committee Chair
Garner, Harold Ray Committee Member
Pérez-Quiñones, Manuel A. Committee Member
Keywords
  • File Streaming
  • 3D Interaction
  • Genomic Visualization
  • Genome Browser
Date of Defense 2012-04-23
Availability restricted
Abstract
With the advent of high throughput sequencing technologies over the past decade there has been a surge in the amount of genomic data that needs to be analyzed and interpreted. Despite the availability of software frameworks such as the Genome Analysis Toolkit, data interpretation and analysis still requires human intervention and refinement. Genome browsers enable developers and users of sequence analysis tools to visualize, compare, and better interpret genomic data such as gene expression and functional annotations. We developed a next generation cross platform web-based genome browser, NextBrowse, for visualizing General Feature Format and Binary Alignment Map files. NextBrowse uses advanced visualization techniques such as 3D feature selection and transparency based on mapping quality, and improved Graphical User Interface elements such as individual track searching and textual and graphical reference location. NextBrowse is the first genome browser to allow BAM files to be streamed and visualized, the first genome browser to employ security measures, and the first to use only client side rendering. NextBrowse takes advantage of the open-source community, allowing developers and users to extend the project to fit their needs. NextBrowse along with all documentation is available for use at http://www.nextbrowse.vbi.vt.edu.
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[VT] Whisenhunt_PJ_T_2012.pdf 4.07 Mb 00:18:49 00:09:41 00:08:28 00:04:14 00:00:21
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