Year of Award


Document Type


Degree Type

Master of Science (MS)

Degree Name

Computer Science

Department or School/College

Computer Science

Committee Chair

Travis Wheeler

Commitee Members

Travis Wheeler, Jesse Johnson, Robert Hubley


annotation, adjudication, transposable element, homologous recombination, gene conversion


University of Montana

Subject Categories



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.



© Copyright 2021 Kaitlin Carey