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Publication type: Article in scientific journal
Type of review: Peer review (publication)
Title: TRAL : tandem repeat annotation library
Authors: Schaper, Elke
Korsunsky, Alexander
Pečerska, Jūlija
Messina, Antonio
Murri, Riccardo
Stockinger, Heinz
Zoller, Stefan
Xenarios, Ioannis
Anisimova, Maria
DOI: 10.21256/zhaw-3884
Published in: Bioinformatics
Volume(Issue): 31
Issue: 18
Page(s): 3051
Pages to: 3053
Issue Date: 2015
Publisher / Ed. Institution: Oxford University Press
ISSN: 1367-4803
Language: English
Subjects: Molecular sequence; Profile hidden Markov models; Tandem repeat; Bioinformatics
Subject (DDC): 004: Computer science
572: Biochemistry
Abstract: 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.
Further description: Erworben im Rahmen der Schweizer Nationallizenzen (
Fulltext version: Published version
License (according to publishing contract): Licence according to publishing contract
Restricted until: 2019-01-01
Departement: Life Sciences and Facility Management
Organisational Unit: Institute of Computational Life Sciences (ICLS)
Appears in collections:Publikationen Life Sciences und Facility Management

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