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      SynVisio: A Multiscale Tool to Explore Genomic Conservation

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      BANDI-THESIS-2020.pdf (14.63Mb)
      Date
      2020-06-22
      Author
      Bandi, Venkat Kiran
      ORCID
      0000-0002-4729-2261
      Type
      Thesis
      Degree Level
      Masters
      Metadata
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      Abstract
      Comparative analysis of genomes is an important area in biological research that can shed light on an organism's internal functions and evolutionary history. It involves comparing two or more genomes to identify similar regions that can indicate shared ancestry and in turn conservation of genetic information. Due to rapid advancements in sequencing systems, high-resolution genome data is readily available for a wide range of species, and comparative analysis of this data can offer crucial evolutionary insights that can be applied in plant breeding and medical research. Visualizing the location, size, and orientation of conserved regions can assist biological researchers in comparative analysis as it is a tedious process that requires extensive manual interpretation and human judgement. However, visualization tools for the analysis of conserved regions have not kept pace with the increasing availability of information and are not designed to support the diverse use cases of researchers. To address this we gathered feedback from experts in the field, and designed improvements for these tools through novel interaction techniques and visual representations. We then developed SynVisio, a web-based tool for exploring conserved regions at multiple resolutions (genome, chromosome, or gene), with several visual representations and interactive features, to meet the diverse needs of genome researchers. SynVisio supports multi-resolution analysis and interactive filtering as researchers move deeper into the genome. It also supports revisitation to specific interface configurations, and enables loosely-coupled collaboration over the genomic data. An evaluation of the system with five researchers from three expert groups coupled with a longitudinal study of web traffic to the system provides evidence about the success of our system's novel features for interactive exploration of conservation.
      Degree
      Master of Science (M.Sc.)
      Department
      Computer Science
      Program
      Computer Science
      Supervisor
      Gutwin, Carl
      Committee
      McQuillan, Ian; Mondal, Debajyoti; Parkin, Isobel
      Copyright Date
      May 2020
      URI
      http://hdl.handle.net/10388/12895
      Subject
      Interactive visualization
      genomic visualization
      coordinated and multiple views
      synteny
      synvisio
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