NextBrowse: An integrated and interactive web-based genome browser for analyzing and interpreting genomic data

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dc.contributor.authorWhisenhunt, Phillip J.en
dc.contributor.committeechairMittelman, David Alexanderen
dc.contributor.committeememberPérez-Quiñones, Manuel A.en
dc.contributor.committeememberGarner, Harold Rayen
dc.contributor.departmentComputer Scienceen
dc.date.accessioned2014-03-14T21:35:07Zen
dc.date.adate2012-05-29en
dc.date.available2014-03-14T21:35:07Zen
dc.date.issued2012-04-23en
dc.date.rdate2012-05-29en
dc.date.sdate2012-04-30en
dc.description.abstractWith 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.en
dc.description.degreeMaster of Scienceen
dc.identifier.otheretd-04302012-125308en
dc.identifier.sourceurlhttp://scholar.lib.vt.edu/theses/available/etd-04302012-125308/en
dc.identifier.urihttp://hdl.handle.net/10919/42371en
dc.publisherVirginia Techen
dc.relation.haspartWhisenhunt_PJ_T_2012.pdfen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectFile Streamingen
dc.subject3D Interactionen
dc.subjectGenomic Visualizationen
dc.subjectGenome Browseren
dc.titleNextBrowse: An integrated and interactive web-based genome browser for analyzing and interpreting genomic dataen
dc.typeThesisen
thesis.degree.disciplineComputer Scienceen
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen
thesis.degree.levelmastersen
thesis.degree.nameMaster of Scienceen

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