The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Gene and translation initiation site prediction in metagenomic sequences
Open accessAbstract
Motivation: Gene prediction in metagenomic sequences remains a difficult problem. Current sequencing technologies do not achieve sufficient coverage to assemble the individual genomes in a typical sample; consequently, sequencing runs produce a large number of short sequences whose exact origin is unknown. Since these sequences are usually smaller than the average length of a gene, algorithms must make predictions based on very little data. Results: We present MetaProdigal, a metagenomic version of the gene prediction program Prodigal, that can identify genes in short, anonymous coding sequences with a high degree of accuracy. The novel value of the method consists of enhanced translation initiation site identification, ability to identify sequences that use alternate genetic codes and confidence values for each gene call. We compare the results of MetaProdigal with other methods and conclude with a discussion of future improvements. Availability: The Prodigal software is freely available under the General Public License from http://code.google.com/p/prodigal/. Contact: hyattpd@ornl.gov Supplementary Information: Supplementary data are available at Bioinformatics online.
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Citations
Cites
NCBI Reference Sequences: current status, policy and new initiatives
Pruitt, K. D., Tatusova, T., Klimke, W., & Maglott, D. R. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn721 · Cited by 736 · cited 1×
“In order to generate these training files, we turned to NCBI's Refseq repository, which, as of September 2010, contained 1415 genome sequences of 500,000 bases or greater (Pruitt et al., 2009).”
Method
Cited by
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496
metaSPAdes: a new versatile metagenomic assembler
Nurk, S., Meleshko, D., Korobeynikov, A., & Pevzner, P. A. (2017) · Genome Research · doi:10.1101/gr.213959.116 · Cited by 4,496
Shotgun metagenomics, from sampling to analysis
Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017) · Nature Biotechnology · doi:10.1038/nbt.3935 · Cited by 2,202
CheckV assesses the quality and completeness of metagenome-assembled viral genomes
Nayfach, S., Camargo, A. P., Schulz, F., Eloe-Fadrosh, E., Roux, S., & Kyrpides, N. C. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-00774-7 · Cited by 1,750
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
(2017) · doi:10.1038/s41564-018-0171-1 · Cited by 1,742
Metadata
- Authors
- Hyatt, D., LoCascio, P. F., Hauser, L. J., & Uberbacher, E. C.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-07-12
- Volume
- 28
- Issue
- 17
- Pages
- 2223-2230
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2168330474
- Cited by
- 651
- References
- 1
- FWCI
- 4.30
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Hyatt, D., LoCascio, P. F., Hauser, L. J., & Uberbacher, E. C. (2012). Gene and translation initiation site prediction in metagenomic sequences. Bioinformatics. https://doi.org/10.1093/bioinformatics/bts429
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