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

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.Bachelor of Scienc