The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
TEclass—a tool for automated classification of unknown eukaryotic transposable elements
Open accessAbstract
Motivation: The large number of sequenced genomes required the development of software that reconstructs the consensus sequences of transposons and other repetitive elements. However, the available tools usually focus on the accurate identification of raw repeats and provide no information about the taxonomic position of the reconstructed consensi. TEclass is a tool to classify unknown transposable elements into their four main functional categories, which reflect their mode of transposition: DNA transposons, long terminal repeats (LTRs), long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs). TEclass uses machine learning support vector machine (SVM) for classification based on oligomer frequencies. It achieves 90–97% accuracy in the classification of novel DNA and LTR repeats, and 75% for LINEs and SINEs. Availability: http://www.compgen.uni-muenster.de/teclass, stand alone program upon request. Contact: abrusan@uni-muenster.de
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Cites
LIBSVM: A library for support vector machines
Chang, C.-C., & Lin, C.-J. (2011) · ACM Transactions on Intelligent Systems and Technology · doi:10.1145/1961189.1961199 · Cited by 40,918
Cited by
Gan, P., Ikeda, K., Irieda, H., Narusaka, M., O'Connell, R. J., Narusaka, Y., Takano, Y., Kubo, Y., & Shirasu, K. (2013) · New Phytologist · doi:10.1111/nph.12085 · Cited by 379
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Jebb, D., Huang, Z., Pippel, M., Hughes, G. M., Lavrichenko, K., Devanna, P., Winkler, S., Jermiin, L. S., Skirmuntt, E. C., Katzourakis, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2486-3 · Cited by 361
PASTEC: An Automatic Transposable Element Classification Tool
Hoede, C., Arnoux, S., Moisset, M., Chaumier, T., Inizan, O., Jamilloux, V., & Quesneville, H. (2014) · PLoS ONE · doi:10.1371/journal.pone.0091929 · Cited by 310
Makałowski, W., Gotea, V., Pande, A., & Makałowska, I. (2019) · Methods in Molecular Biology · doi:10.1007/978-1-4939-9074-0_6 · Cited by 127
Self-citationA chromosome-level reference genome assembly of the Reeve’s moray eel (Gymnothorax reevesii)
Zhang, K., Huang, Y., Zhang, Y., Liang, R., Li, Q., Li, R., Zhao, X., Bian, C., Chen, Y., Wu, J., et al. (2023) · Scientific Data · doi:10.1038/s41597-023-02394-7 · Cited by 8
Metadata
- Authors
- Abrusán, G., Grundmann, N., DeMester, L., & Makalowski, W.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-04-05
- Volume
- 25
- Issue
- 10
- Pages
- 1329-1330
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2132141594
- Cited by
- 368
- References
- 1
- FWCI
- 10.58
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Abrusán, G., Grundmann, N., DeMester, L., & Makalowski, W. (2009). TEclass—a tool for automated classification of unknown eukaryotic transposable elements. Bioinformatics. https://doi.org/10.1093/bioinformatics/btp084
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