The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Identifying bacterial genes and endosymbiont DNA with Glimmer
Open accessAbstract
Motivation: The Glimmer gene-finding software has been successfully used for finding genes in bacteria, archæa and viruses representing hundreds of species. We describe several major changes to the Glimmer system, including improved methods for identifying both coding regions and start codons. We also describe a new module of Glimmer that can distinguish host and endosymbiont DNA. This module was developed in response to the discovery that eukaryotic genome sequencing projects sometimes inadvertently capture the DNA of intracellular bacteria living in the host. Results: The new methods dramatically reduce the rate of false-positive predictions, while maintaining Glimmer's 99% sensitivity rate at detecting genes in most species, and they find substantially more correct start sites, as measured by comparisons to known and well-curated genes. We show that our interpolated Markov model (IMM) DNA discriminator correctly separated 99% of the sequences in a recent genome project that produced a mixture of sequences from the bacterium Prochloron didemni and its sea squirt host, Lissoclinum patella. Availability: Glimmer is OSI Certified Open Source and available at http://cbcb.umd.edu/software/glimmer Contact: adelcher@umiacs.umd.edu
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Cites
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“This similarity often breaks down near the 50 end of the transcript, which also tends to be the region where gene finders disagree on the precise position of the start codon.”
Background
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Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice
Ridaura, V. K., Faith, J. J., Rey, F. E., Cheng, J., Duncan, A. E., Kau, A. L., Griffin, N. W., Lombard, V., Henrissat, B., Bain, J. R., et al. (2013) · Science · doi:10.1126/science.1241214 · Cited by 3,788
Current challenges and best-practice protocols for microbiome analysis
Bharti, R., & Grimm, D. G. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbz155 · Cited by 592
Sun, Z., Harris, H. M. B., McCann, A., Guo, C., Argimón, S., Zhang, W., Yang, X., Jeffery, I. B., Cooney, J. C., Kagawa, T. F., et al. (2015) · Nature Communications · doi:10.1038/ncomms9322 · Cited by 543
Lawley, T. D., Clare, S., Walker, A. W., Stares, M. D., Connor, T. R., Raisen, C., Goulding, D., Rad, R., Schreiber, F., Brandt, C., et al. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1002995 · Cited by 540
The role of the gut microbiome in the healthy adult status
D’Argenio, V., & Salvatore, F. (2015) · Clinica Chimica Acta · doi:10.1016/j.cca.2015.01.003 · Cited by 492
Metadata
- Authors
- Delcher, A. L., Bratke, K. A., Powers, E. C., & Salzberg, S. L.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-01-19
- Volume
- 23
- Issue
- 6
- Pages
- 673-679
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2105199251
- Cited by
- 3,134
- References
- 2
- FWCI
- 20.35
- Type
- journal article
- Language
- en
- Open access
- hybrid
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