{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T13:16:35Z","timestamp":1774790195717,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Currently, more than 40 sequence tandem repeat detectors are published, providing heterogeneous, partly complementary, partly conflicting results.<\/jats:p>\n               <jats:p>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\u2009085 sequences in UniProtKB\/Swiss-Prot. The researcher can use these results to predict run-times for specific datasets, and to choose annotation complexity accordingly.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Contact: \u00a0elke.schaper@isb-sib.ch<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv306","type":"journal-article","created":{"date-parts":[[2015,5,19]],"date-time":"2015-05-19T00:50:48Z","timestamp":1431996648000},"page":"3051-3053","source":"Crossref","is-referenced-by-count":17,"title":["TRAL: tandem repeat annotation library"],"prefix":"10.1093","volume":"31","author":[{"given":"Elke","family":"Schaper","sequence":"first","affiliation":[{"name":"1 Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 2SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 3Department of Computer Science, ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland, 4Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, 5Department of Biosystems Science and Engineering, ETH Z\u00fcrich, 4058 Basel, Switzerland, 6Services and Support for Science IT, University of Z\u00fcrich, 8057 Z\u00fcrich, Switzerland and 7Institute of Applied Simulations, School of Life Sciences und Facility Management, Z\u00fcrich University of Applied Sciences, 8820 W\u00e4denswil, Switzerland"},{"name":"1 Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 2SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 3Department of Computer Science, ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland, 4Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, 5Department of Biosystems Science and Engineering, ETH Z\u00fcrich, 4058 Basel, Switzerland, 6Services and Support for Science IT, University of Z\u00fcrich, 8057 Z\u00fcrich, Switzerland and 7Institute of Applied Simulations, School of Life Sciences und Facility Management, Z\u00fcrich University of Applied Sciences, 8820 W\u00e4denswil, Switzerland"},{"name":"1 Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 2SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 3Department of Computer Science, ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland, 4Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, 5Department of Biosystems Science and Engineering, ETH Z\u00fcrich, 4058 Basel, Switzerland, 6Services and Support for Science IT, University of Z\u00fcrich, 8057 Z\u00fcrich, Switzerland and 7Institute of Applied Simulations, School of Life Sciences und Facility Management, Z\u00fcrich University of Applied Sciences, 8820 W\u00e4denswil, Switzerland"}]},{"given":"Alexander","family":"Korsunsky","sequence":"additional","affiliation":[{"name":"1 Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 2SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 3Department of Computer Science, ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland, 4Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, 5Department of Biosystems Science and Engineering, ETH Z\u00fcrich, 4058 Basel, Switzerland, 6Services and Support for Science IT, University of Z\u00fcrich, 8057 Z\u00fcrich, Switzerland and 7Institute of Applied Simulations, School of Life Sciences und Facility Management, Z\u00fcrich University of Applied Sciences, 8820 W\u00e4denswil, Switzerland"}]},{"given":"J\u016blija","family":"Pe\u010derska","sequence":"additional","affiliation":[{"name":"1 Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 2SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 3Department of Computer Science, ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland, 4Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, 5Department of Biosystems Science and Engineering, ETH Z\u00fcrich, 4058 Basel, Switzerland, 6Services and Support for Science IT, University of Z\u00fcrich, 8057 Z\u00fcrich, Switzerland and 7Institute of Applied Simulations, School of Life Sciences und Facility Management, Z\u00fcrich University of Applied Sciences, 8820 W\u00e4denswil, Switzerland"},{"name":"1 Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 2SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 3Department of Computer Science, ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland, 4Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, 5Department of Biosystems Science and Engineering, ETH Z\u00fcrich, 4058 Basel, Switzerland, 6Services and Support for Science IT, University of Z\u00fcrich, 8057 Z\u00fcrich, Switzerland and 7Institute of Applied Simulations, School of Life Sciences und Facility Management, Z\u00fcrich University of Applied Sciences, 8820 W\u00e4denswil, Switzerland"},{"name":"1 Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 2SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 3Department of Computer Science, ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland, 4Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, 5Department of Biosystems Science and Engineering, ETH Z\u00fcrich, 4058 Basel, Switzerland, 6Services and Support for Science IT, University of Z\u00fcrich, 8057 Z\u00fcrich, Switzerland and 7Institute of Applied Simulations, School of Life Sciences und Facility Management, Z\u00fcrich University of Applied Sciences, 8820 W\u00e4denswil, Switzerland"}]},{"given":"Antonio","family":"Messina","sequence":"additional","affiliation":[{"name":"1 Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 2SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 3Department of Computer Science, ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland, 4Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, 5Department of Biosystems Science and Engineering, ETH Z\u00fcrich, 4058 Basel, Switzerland, 6Services and Support for Science IT, University of Z\u00fcrich, 8057 Z\u00fcrich, Switzerland and 7Institute of Applied Simulations, School of Life Sciences und Facility Management, Z\u00fcrich University of Applied Sciences, 8820 W\u00e4denswil, Switzerland"}]},{"given":"Riccardo","family":"Murri","sequence":"additional","affiliation":[{"name":"1 Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 2SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 3Department of Computer Science, ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland, 4Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, 5Department of Biosystems Science and Engineering, ETH Z\u00fcrich, 4058 Basel, Switzerland, 6Services and Support for Science IT, University of Z\u00fcrich, 8057 Z\u00fcrich, Switzerland and 7Institute of Applied Simulations, School of Life Sciences und Facility Management, Z\u00fcrich University of Applied Sciences, 8820 W\u00e4denswil, Switzerland"}]},{"given":"Heinz","family":"Stockinger","sequence":"additional","affiliation":[{"name":"1 Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 2SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 3Department of Computer Science, ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland, 4Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, 5Department of Biosystems Science and Engineering, ETH Z\u00fcrich, 4058 Basel, Switzerland, 6Services and Support for Science IT, University of Z\u00fcrich, 8057 Z\u00fcrich, Switzerland and 7Institute of Applied Simulations, School of Life Sciences und Facility Management, Z\u00fcrich University of Applied Sciences, 8820 W\u00e4denswil, Switzerland"}]},{"given":"Stefan","family":"Zoller","sequence":"additional","affiliation":[{"name":"1 Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 2SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 3Department of Computer Science, ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland, 4Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, 5Department of Biosystems Science and Engineering, ETH Z\u00fcrich, 4058 Basel, Switzerland, 6Services and Support for Science IT, University of Z\u00fcrich, 8057 Z\u00fcrich, Switzerland and 7Institute of Applied Simulations, School of Life Sciences und Facility Management, Z\u00fcrich University of Applied Sciences, 8820 W\u00e4denswil, Switzerland"},{"name":"1 Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 2SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 3Department of Computer Science, ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland, 4Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, 5Department of Biosystems Science and Engineering, ETH Z\u00fcrich, 4058 Basel, Switzerland, 6Services and Support for Science IT, University of Z\u00fcrich, 8057 Z\u00fcrich, Switzerland and 7Institute of Applied Simulations, School of Life Sciences und Facility Management, Z\u00fcrich University of Applied Sciences, 8820 W\u00e4denswil, Switzerland"}]},{"given":"Ioannis","family":"Xenarios","sequence":"additional","affiliation":[{"name":"1 Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 2SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 3Department of Computer Science, ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland, 4Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, 5Department of Biosystems Science and Engineering, ETH Z\u00fcrich, 4058 Basel, Switzerland, 6Services and Support for Science IT, University of Z\u00fcrich, 8057 Z\u00fcrich, Switzerland and 7Institute of Applied Simulations, School of Life Sciences und Facility Management, Z\u00fcrich University of Applied Sciences, 8820 W\u00e4denswil, Switzerland"},{"name":"1 Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, 2SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, 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