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PolyA: a tool for adjudicating competing annotations of biological sequences

Kaitlin M. Carey, Robert Hubley, George T. Lesica, Daniel Olson, Jack W. Roddy, Jeb Rosen, Audrey Shingleton, Arian F. Smit, View ORCID ProfileTravis J. Wheeler
doi: https://doi.org/10.1101/2021.02.13.430877
Kaitlin M. Carey
1Department of Computer Science, University of Montana, Missoula, MT, USA
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Robert Hubley
2Institute for Systems Biology, Seattle, WA, USA
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George T. Lesica
1Department of Computer Science, University of Montana, Missoula, MT, USA
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Daniel Olson
1Department of Computer Science, University of Montana, Missoula, MT, USA
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Jack W. Roddy
1Department of Computer Science, University of Montana, Missoula, MT, USA
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Jeb Rosen
2Institute for Systems Biology, Seattle, WA, USA
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Audrey Shingleton
1Department of Computer Science, University of Montana, Missoula, MT, USA
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Arian F. Smit
2Institute for Systems Biology, Seattle, WA, USA
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Travis J. Wheeler
1Department of Computer Science, University of Montana, Missoula, MT, USA
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  • ORCID record for Travis J. Wheeler
  • For correspondence: Travis.Wheeler@umontana.edu
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Abstract

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, we 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.

Competing Interest Statement

The authors have declared no competing interest.

  • Abbreviations

    TE
    transposable element
    STR
    short tandem repeat
    RM
    RepeatMasker
    DP
    Dynamic programming
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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    Posted February 14, 2021.
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    PolyA: a tool for adjudicating competing annotations of biological sequences
    Kaitlin M. Carey, Robert Hubley, George T. Lesica, Daniel Olson, Jack W. Roddy, Jeb Rosen, Audrey Shingleton, Arian F. Smit, Travis J. Wheeler
    bioRxiv 2021.02.13.430877; doi: https://doi.org/10.1101/2021.02.13.430877
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    PolyA: a tool for adjudicating competing annotations of biological sequences
    Kaitlin M. Carey, Robert Hubley, George T. Lesica, Daniel Olson, Jack W. Roddy, Jeb Rosen, Audrey Shingleton, Arian F. Smit, Travis J. Wheeler
    bioRxiv 2021.02.13.430877; doi: https://doi.org/10.1101/2021.02.13.430877

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