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TRAL: tandem repeat annotation library.

Elke Schaper1, Alexander Korsunsky2, Jūlija Pečerska1

  • 1Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wäde

Bioinformatics (Oxford, England)
|May 20, 2015
PubMed
Summary
This summary is machine-generated.

TRAL is a new library for analyzing tandem repeats, consolidating results from multiple detectors. It improves accuracy by filtering false positives and refining annotations using circular profile hidden Markov models.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Numerous tandem repeat (TR) detection tools exist, yielding inconsistent and conflicting results.
  • The heterogeneity of TR detection outputs complicates downstream analysis and interpretation.

Purpose of the Study:

  • To introduce TRAL, a versatile library for processing and analyzing TR detection outputs.
  • To provide a standardized framework for evaluating and refining TR annotations.

Main Methods:

  • TRAL integrates multiple TR detection tools and parses their outputs.
  • It implements annotation clustering, false positive filtering using statistical frameworks, and a novel TR annotation/refinement module based on circular profile hidden Markov models (cpHMMs).

Main Results:

  • TRAL was used to evaluate a multi-step TR annotation workflow on over 547,000 UniProtKB/Swiss-Prot sequences.
  • The study provides insights into the performance of TR annotation workflows, enabling prediction of run-times and selection of annotation complexity.

Conclusions:

  • TRAL offers a comprehensive solution for managing and analyzing diverse TR detection data.
  • The library facilitates robust TR annotation and aids researchers in optimizing their analysis pipelines for large-scale genomic datasets.