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ULTRA: A Model Based Tool to Detect Tandem Repeats.

Daniel Olson1, Travis Wheeler2

  • 1University of Montana, Missoula, Montana daniel.olson@umontana.edu.

ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine
|May 14, 2019
PubMed
Summary

This study introduces ULTRA, a new hidden Markov model tool for detecting decayed tandem repeats in biological sequences. ULTRA offers improved sensitivity and low false annotation rates, outperforming existing methods like TRF.

Keywords:
Annotation ErrorSequence AlignmentTandem Repeats

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Tandem repeats in biological sequences are repetitive patterns that can decay over time.
  • Degenerate tandem repeats can lead to false signals of sequence homology, complicating sequence annotation.
  • Accurate detection of these repeats is crucial for reliable genomic analysis.

Purpose of the Study:

  • To develop and implement a novel hidden Markov model for enhanced detection of tandem repeats, particularly degenerate ones.
  • To create a tool (ULTRA) that improves sensitivity and reduces false annotation rates in repeat detection.
  • To provide a computationally efficient tool for tandem repeat masking in genomic sequences.

Main Methods:

  • Implementation of a new hidden Markov model tailored for detecting decayed repetitive regions.
  • Development of the ULTRA software tool for tandem repeat analysis.
  • Benchmarking ULTRA against existing tools like TRF on typical genomic sequences.

Main Results:

  • The new hidden Markov model demonstrates substantially improved sensitivity in labeling decayed repetitive regions.
  • ULTRA exhibits low and reliable false annotation rates across diverse sequence compositions.
  • ULTRA's performance in terms of time and memory is competitive with the widely used TRF tool.
  • The tool produces scores that follow a stable distribution, aiding in reliable interpretation.

Conclusions:

  • ULTRA provides a sensitive and accurate method for detecting degenerate tandem repeats in biological sequences.
  • The tool offers a viable, efficient alternative to existing repeat masking methods.
  • ULTRA's open-source release and model architecture facilitate its integration into broader sequence analysis pipelines.