The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Capturing Whole-Genome Characteristics in Short Sequences Using a Naïve Bayesian Classifier
Open accessAbstract
Bacterial genomes have diverged during evolution, resulting in clearcut differences in their nucleotide composition, such as their GC content. The analysis of complete sequences of bacterial genomes also reveals the presence of nonrandom sequence variation, manifest in the frequency profile of specific short oligonucleotides. These frequency profiles constitute highly specific genomic signatures. Based on these differences in oligonucleotide frequency between bacterial genomes, we investigated the possibility of predicting the genome of origin for a specific genomic sequence. To this end, we developed a naïve Bayesian classifier and systematically analyzed 28 eubacterial and archaeal genomes. We found that sequences as short as 400 bases could be correctly classified with an accuracy of 85%. We then applied the classifier to the identification of horizontal gene transfer events in whole-genome sequences and demonstrated the validity of our approach by correctly predicting the transfer of both the superoxide dismutase (sodC) and the bioC gene from Haemophilus influenzae to Neisseria meningitis, correctly identifying both the donor and recipient species. We believe that this classification methodology could be a valuable tool in biodiversity studies.
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Cites
Comparative Genomics of the Eukaryotes
Rubin, G. M., Yandell, M. D., Wortman, J. R., Gabor, G. L., Miklos, Nelson, C. R., Hariharan, I. K., Fortini, M. E., Li, P. W., Apweiler, R., et al. (2000) · Science · doi:10.1126/science.287.5461.2204 · Cited by 1,698 · cited 1×
“Recent investigations have reported differences in both the subsets of proteins the genomes encode (Rubin et al. 2000) and the frequency of occurrence of many short oligonucleotides (Karlin and Burge 1995), hereafter called “motifs”.”
BackgroundA Sequential Algorithm for Training Text Classifiers
Lewis, D. D., & Gale, W. A. (1994) · SIGIR ’94 · doi:10.1007/978-1-4471-2099-5_1 · Cited by 1,208
Dinucleotide relative abundance extremes: a genomic signature
Kariin, S., & Burge, C. (1995) · Trends in Genetics · doi:10.1016/s0168-9525(00)89076-9 · Cited by 701
Cited by
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00062-07 · Cited by 19,885
Community structure and metabolism through reconstruction of microbial genomes from the environment
Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., & Banfield, J. F. (2004) · Nature · doi:10.1038/nature02340 · Cited by 2,417
Metagenomic Analyses: Past and Future Trends
Simon, C., & Daniel, R. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.02345-10 · Cited by 731
Vernikos, G. S., & Parkhill, J. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl369 · Cited by 494
A Bioinformatician's Guide to Metagenomics
Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K., & Hugenholtz, P. (2008) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00009-08 · Cited by 490
Metadata
- Authors
- Sandberg, R., Winberg, G., Bränden, C.-I., Kaske, A., Ernberg, I., & Cöster, J.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2001-08-01
- Volume
- 11
- Issue
- 8
- Pages
- 1404-1409
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- OpenAlex
- W2140320695
- Cited by
- 210
- References
- 3
- Type
- posted content
- Language
- en
- Open access
- bronze
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