Please use this identifier to cite or link to this item:
https://doi.org/10.21256/zhaw-3884
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: | 10.1093/bioinformatics/btv306 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 1367-4811 |
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 (http://www.nationallizenzen.ch) |
URI: | https://digitalcollection.zhaw.ch/handle/11475/8265 |
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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Schaper, E., Korsunsky, A., Pečerska, J., Messina, A., Murri, R., Stockinger, H., Zoller, S., Xenarios, I., & Anisimova, M. (2015). TRAL : tandem repeat annotation library. Bioinformatics, 31(18), 3051–3053. https://doi.org/10.1093/bioinformatics/btv306
Schaper, E. et al. (2015) ‘TRAL : tandem repeat annotation library’, Bioinformatics, 31(18), pp. 3051–3053. Available at: https://doi.org/10.1093/bioinformatics/btv306.
E. Schaper et al., “TRAL : tandem repeat annotation library,” Bioinformatics, vol. 31, no. 18, pp. 3051–3053, 2015, doi: 10.1093/bioinformatics/btv306.
SCHAPER, Elke, Alexander KORSUNSKY, Jūlija PEČERSKA, Antonio MESSINA, Riccardo MURRI, Heinz STOCKINGER, Stefan ZOLLER, Ioannis XENARIOS und Maria ANISIMOVA, 2015. TRAL : tandem repeat annotation library. Bioinformatics. 2015. Bd. 31, Nr. 18, S. 3051–3053. DOI 10.1093/bioinformatics/btv306
Schaper, Elke, Alexander Korsunsky, Jūlija Pečerska, Antonio Messina, Riccardo Murri, Heinz Stockinger, Stefan Zoller, Ioannis Xenarios, and Maria Anisimova. 2015. “TRAL : Tandem Repeat Annotation Library.” Bioinformatics 31 (18): 3051–53. https://doi.org/10.1093/bioinformatics/btv306.
Schaper, Elke, et al. “TRAL : Tandem Repeat Annotation Library.” Bioinformatics, vol. 31, no. 18, 2015, pp. 3051–53, https://doi.org/10.1093/bioinformatics/btv306.
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