The DOI matches its Crossref record; 30 of the 30 references it cites were found in a registry or an index.
Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands
Open accessAbstract
Motivation: There is a growing literature on the detection of Horizontal Gene Transfer (HGT) events by means of parametric, non-comparative methods. Such approaches rely only on sequence information and utilize different low and high order indices to capture compositional deviation from the genome backbone; the superiority of the latter over the former has been shown elsewhere. However even high order k-mers may be poor estimators of HGT, when insufficient information is available, e.g. in short sliding windows. Most of the current HGT prediction methods require pre-existing annotation, which may restrict their application on newly sequenced genomes. Results: We introduce a novel computational method, Interpolated Variable Order Motifs (IVOMs), which exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared with fixed-order methods. For optimal localization of the boundaries of each predicted region, a second order, two-state hidden Markov model (HMM) is implemented in a change-point detection framework. We applied the IVOM approach to the genome of Salmonella enterica serovar Typhi CT18, a well-studied prokaryote in terms of HGT events, and we show that the IVOMs outperform state-of-the-art low and high order motif methods predicting not only the already characterized Salmonella Pathogenicity Islands (SPI-1 to SPI-10) but also three novel SPIs (SPI-15, SPI-16, SPI-17) and other HGT events. Availability: The software is available under a GPL license as a standalone application at Contact: gsv@sanger.ac.uk Supplementary Information: Supplementary data are available at Bioinformatics online.
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Cited by
Stinear, T. P., Seemann, T., Harrison, P. F., Jenkin, G. A., Davies, J. K., Johnson, P. D. R., Abdellah, Z., Arrowsmith, C., Chillingworth, T., Churcher, C., et al. (2008) · Genome Research · doi:10.1101/gr.075069.107 · Cited by 570
Self-citationNon Mycobacterial Virulence Genes in the Genome of the Emerging Pathogen Mycobacterium abscessus
Ripoll, F., Pasek, S., Schenowitz, C., Dossat, C., Barbe, V., Rottman, M., Macheras, E., Heym, B., Herrmann, J.-L., Daffé, M., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0005660 · Cited by 388
Langille, M. G. I., & Brinkman, F. S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp030 · Cited by 388
Winstanley, C., Langille, M. G. I., Fothergill, J. L., Kukavica-Ibrulj, I., Paradis-Bleau, C., Sanschagrin, F., Thomson, N. R., Winsor, G. L., Quail, M. A., Lennard, N., et al. (2009) · Genome Research · doi:10.1101/gr.086082.108 · Cited by 339
Self-citationThe Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri
Frese, S. A., Benson, A. K., Tannock, G. W., Loach, D. M., Kim, J., Zhang, M., Oh, P. L., Heng, N. C. K., Patil, P. B., Juge, N., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001314 · Cited by 310
Metadata
- Authors
- Vernikos, G. S., & Parkhill, J.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-07-12
- Volume
- 22
- Issue
- 18
- Pages
- 2196-2203
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2108228587
- Cited by
- 494
- References
- 30
- FWCI
- 5.89
- Type
- journal article
- Language
- en
- Open access
- hybrid
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