The DOI matches its Crossref record; 17 of the 17 references it cites were found in a registry or an index.
TRAL: tandem repeat annotation library
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. 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
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“Further, TRAL allows for evolutionary analyses of the annotated repeats, such as evaluating whether a TR region may be under selection.”
From Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases (2019) · cites this paper as [91]
In the citing paper
“The TRAL library can be easily included in developing new pipelines for genome assembly and repeat annotation.”
From Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases (2019) · cites this paper as [91]
In the citing paper
“Currently, such procedure can be implemented using the Tandem Repeat Annotation Library (TRAL) (91).”
From Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases (2019) · cites this paper as [91]
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Citations
Cites
The Pfam Protein Families Database
Bateman, A. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.276 · Cited by 14,000
Tandem repeats finder: a program to analyze DNA sequences
Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374
HMMER web server: interactive sequence similarity searching
Finn, R. D., Clements, J., & Eddy, S. R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr367 · Cited by 5,952
Eddy, S. R. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.755 · Cited by 5,515
The Pfam protein families database
Punta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1065 · Cited by 3,719
A flexible motif search technique based on generalized profiles
Bucher, P., Karplus, K., Moeri, N., & Hofmann, K. (1996) · Computers & Chemistry · doi:10.1016/s0097-8485(96)80003-9 · Cited by 316
T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm
Jorda, J., & Kajava, A. V. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp482 · Cited by 185
Newman, A. M., & Cooper, J. B. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-382 · Cited by 172
De novo identification of highly diverged protein repeats by probabilistic consistency
Biegert, A., & Söding, J. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn039 · Cited by 152
Tracking repeats using significance and transitivity
Szklarczyk, R., & Heringa, J. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth911 · Cited by 142
Cited by
Tørresen, O. K., Star, B., Mier, P., Andrade-Navarro, M. A., Bateman, A., Jarnot, P., Gruca, A., Grynberg, M., Kajava, A. V., Promponas, V. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz841 · Cited by 347
Self-citationBuilding alternative splicing and evolution-aware sequence-structure maps for protein repeats
Szatkownik, A., Zea, D. J., Richard, H., & Laine, E. (2023) · Journal of Structural Biology · doi:10.1016/j.jsb.2023.107997 · Cited by 1
Metadata
- Authors
- Schaper, E., Korsunsky, A., Pečerska, J., Messina, A., Murri, R., Stockinger, H., Zoller, S., Xenarios, I., & Anisimova, M.
- Affiliations
- 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 Zürich, 8092 Zürich, Switzerland, 4Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, 5Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, 6Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and 7Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-05-18
- Volume
- 31
- Issue
- 18
- Pages
- 3051-3053
- ISSN
- 1367-4811
- 1367-4803
- Cited by
- 19
- References
- 17
- Language
- en
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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. https://doi.org/10.1093/bioinformatics/btv306
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