A Method for Construction of a Splice Graph from RNA Sequence Data Public Deposited

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Last Modified
  • February 26, 2019
Creator
  • Bogerd, Jacob
    • Affiliation: College of Arts and Sciences, Department of Computer Science
Abstract
  • Although genetic information in the cell is stored in DNA, the RNA transcripts obtained from DNA indicate which genes are actively transcribed. Modern high-throughput sequencing techniques allow accurate sequencing of short RNA fragments, which may then be aligned to a reference genome. These alignments can be summarized by constructing a "splice graph", in which nodes represent genomic coordinates and edges represent sequences that are retained or spliced out of observed transcripts. Each full-length transcript corresponds to a path through the graph. I have written software to build a splice graph from a collection of short reads aligned to a reference genome. This software incorporates variants observed relative to the reference genome as additional paths. I have also written tools to manipulate and traverse such graphs. An application of this graph is correction of noisy full-length RNA transcripts. Such a transcript may be aligned to paths through the graph in order to identify its original sequence.
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Rights statement
  • In Copyright
Note
  • Funding: None
Advisor
  • Prins, Jan
Degree
  • Bachelor of Science
Honors level
  • Highest Honors
Degree granting institution
  • University of North Carolina at Chapel Hill
Extent
  • 10 p.
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