Year of Award
2024
Document Type
Dissertation
Degree Type
Doctor of Philosophy (PhD)
Degree Name
Cellular, Molecular and Microbial Biology
Department or School/College
Division of Biological Sciences
Committee Chair
Travis Wheeler
Commitee Members
Mark Grimes, Jesse Johnson, Stephen Lodmell, Stephen Sprang
Keywords
Alternative Splicing, Exon Discovery, Intron Splicing, Multiple-Sequence Alignment, Sequence Annotation, Translated Similarity Search
Abstract
Pre-mRNA intron splicing is essential to the production of many eukaryotic proteins, but it is relatively uncommon for sequence analysis tools to account for this process in their methods. In this dissertation I present three tools for biological sequence analysis, demonstrating the benefits that they derive from their explicit awareness of intron splicing. First, I present Mirage2, an updated implementation of the Mirage multiple sequence alignment program, which produces alignments of protein isoforms according to spliced genome mapping coordinates. I then present Diviner, which synthesizes the output data produced by Mirage2 to locate novel coding regions on eukaryotic genomes. Finally, I present splash, which produces spliced translated alignments of protein pHMMs to eukaryotic genomes based on the highly sensitive sequence similarity framework of BATH.
Recommended Citation
Nord, Alexander, "LEAVING THEM IN STITCHES: NOVEL METHODS FOR SPLICE-AWARE SEQUENCE ANNOTATION" (2024). Graduate Student Theses, Dissertations, & Professional Papers. 12385.
https://scholarworks.umt.edu/etd/12385
© Copyright 2024 Alexander Nord