Year of Award
Master of Science (MS)
Department or School/College
Travis Wheeler, Jesse Johnson, Robert Hubley
annotation, adjudication, transposable element, homologous recombination, gene conversion
University of Montana
Annotation of a biological sequence is usually performed by aligning that sequence to a database of known sequence elements. When that database contains elements that are highly similar to each other, the proper annotation may be ambiguous, because several entries in the database produce high-scoring alignments. Typical annotation methods work by assigning a label based on the candidate annotation with the highest alignment score; this can overstate annotation certainty, mislabel boundaries, and fails to identify large scale rearrangements or insertions within the annotated sequence. Here, I present a new software tool, PolyA, that adjudicates between competing alignment-based annotations by computing estimates of annotation confidence, identifying a trace with maximal confidence, and recursively splicing/stitching inserted elements. PolyA communicates annotation certainty, identifies large scale rearrangements, and detects boundaries between neighboring elements.
Carey, Kaitlin, "POLYA: A TOOL FOR ADJUDICATING COMPETING ANNOTATIONS OF BIOLOGICAL SEQUENCES" (2021). Graduate Student Theses, Dissertations, & Professional Papers. 11672.
© Copyright 2021 Kaitlin Carey