TRAL: tandem repeat annotation library.

Schaper E; Korsunsky A; Pečerska J; Messina A; Murri R; Stockinger H; Zoller S; Xenarios I; Anisimova M

doi:10.1093/bioinformatics/btv306

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Journal article

TRAL: tandem repeat annotation library.

Schaper E 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 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
Korsunsky A 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.
Pečerska J 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 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
Messina A 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.
Murri R 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.
Stockinger H 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.
Zoller S 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 Wädenswil, Switzerland.
Xenarios I 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 Wädenswil, Switzerland.
Anisimova M 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 Wädenswil, Switzerland.

2015-05-20

Published in:

Bioinformatics (Oxford, England). - 2015

English MOTIVATION
Currently, more than 40 sequence tandem repeat detectors are published, providing heterogeneous, partly complementary, partly conflicting results.

RESULTS
We present TRAL, a tandem repeat annotation library that allows running and parsing of various detection outputs, clustering of redundant or overlapping annotations, several statistical frameworks for filtering false positive annotations, and importantly a tandem repeat annotation and refinement module based on circular profile hidden Markov models (cpHMMs). Using TRAL, we evaluated the performance of a multi-step tandem repeat annotation workflow on 547 085 sequences in UniProtKB/Swiss-Prot. The researcher can use these results to predict run-times for specific datasets, and to choose annotation complexity accordingly.

AVAILABILITY AND IMPLEMENTATION
TRAL is an open-source Python 3 library and is available, together with documentation and tutorials via http://www.vital-it.ch/software/tral.

CONTACT
elke.schaper@isb-sib.ch.

Language